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Flathead Subbasin Summary

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					             Draft
             Flathead River
             Subbasin Summary

             March 16, 2001


             Prepared for the
             Northwest Power Planning Council


             Subbasin Team Leader
             Lynn Ducharme
             Confederated Salish and Kootenai Tribes of the Flathead Indian
             Reservation

             Contributors (in alphabetical order):
             Dale Becker, Confederated Salish and Kootenai Tribes
             Lynn DuCharme, Confederated Salish and Kootenai Tribes
             Les Evarts, Confederated Salish and Kootenai Tribes
             Grant Grisak, Montana Department of Fish, Wildlife & Parks
             Barry Hansen, Confederated Salish and Kootenai Tribes
             Brian Lipscomb, Confederated Salish and Kootenai Tribes
             Brian Marotz, Montana Department of Fish, Wildlife & Parks
             Clint Muhlfeld, Montana Department of Fish, Wildlife & Parks
             Art Soukkala, Confederated Salish and Kootenai Tribes
             Alan Wood, Montana Department of Fish, Wildlife & Parks

DRAFT: This document has not yet been reviewed or approved by
       the Northwest Power Planning Council.
Flathead River Subbasin Summary
                                                                  Table of Contents

Subbasin Description .......................................................................................................................... 1
       General Description .................................................................................................................... 1
       Subbasin Location .................................................................................................................................... 1
       Drainage Area........................................................................................................................................... 1
       Climate ..................................................................................................................................................... 1
       Topography .............................................................................................................................................. 3
       Geology .................................................................................................................................................... 3
       Hydrology................................................................................................................................................. 3
       Soils .......................................................................................................................................................... 5
       Land Uses ................................................................................................................................................. 5
       Impoundments and Irrigation Projects ...................................................................................................... 6
       Protected Areas ........................................................................................................................................ 8
Fish and Wildlife Resources ............................................................................................................... 8
       Fish and Wildlife Status ............................................................................................................. 8
       Fish ........................................................................................................................................................... 8
       Wildlife................................................................................................................................................... 19
       Habitat Areas and Quality ........................................................................................................ 23
       Fish ......................................................................................................................................................... 23
       Wildlife................................................................................................................................................... 27
       Watershed Assessment ............................................................................................................. 31
       Limiting Factors........................................................................................................................ 35
       Alteration of the Littoral Zone ................................................................................................................ 36
       Altered Hydrograph ................................................................................................................................ 36
       Cultural Eutrophication .......................................................................................................................... 36
       Floodplain Alterations ............................................................................................................................ 37
       Fragmentation of Habitat ........................................................................................................................ 37
       Human/Wildlife Conflicts ...................................................................................................................... 37
       Inundation and Water Fluctuations ......................................................................................................... 37
       Non-native Species Interactions ............................................................................................................. 38
       Sedimentation ......................................................................................................................................... 39
       Temperature Changes ............................................................................................................................. 39
       Vegetation Changes ................................................................................................................................ 39
       Artificial Production ................................................................................................................. 39
       Sekokini Springs Natural Rearing Facility and Interpretive Center ........................................................ 40
       Existing and Past Efforts .......................................................................................................... 41
       Summary of Past Efforts ......................................................................................................................... 41
       Accomplishments by Year ...................................................................................................................... 43
Present Subbasin Management ......................................................................................................... 48
       Existing Management ............................................................................................................... 48
       Federal Government ............................................................................................................................... 50
       Tribes...................................................................................................................................................... 51
       State ........................................................................................................................................................ 52


Flathead Subbasin Summary                                                         i                                                                       3/6/01
        Local Government .................................................................................................................................. 52
       Existing Goals, Objectives, and Strategies ............................................................................... 53
        Headwaters and Associated Uplands (includes all mountain tributaries) ............................................... 53
        Impoundments (includes Hungry Horse Reservoir, Flathead Lake, Swan Lake, and irrigation
        impoundments) ....................................................................................................................................... 54
        Regulated Mainstems (includes South Fork, Upper Flathead, Lower Flathead, Jocko River)............... 55
        Unregulated Mainstems (includes North Fork, Middle Fork, and Swan Rivers) .................................... 56
        Valley Tributaries & Wetlands (includes all valley tributaries and the Whitefish and Stillwater rivers) 57
        Lakes (includes connected and closed-basin lakes) ................................................................................ 58
       Research, Monitoring, and Evaluation Activities ..................................................................... 59
        Fisheries ................................................................................................................................................. 59
        Wildlife................................................................................................................................................... 62
       Statement of Fish and Wildlife Needs ...................................................................................... 64
References ........................................................................................................................................ 68
Subbasin Recommendations ............................................................................................................. 75
       FY 2001 Projects Proposals Review......................................................................................... 75
       Projects and Budgets................................................................................................................. 75
        Continuation of Ongoing Projects .......................................................................................................... 75
        New Projects .......................................................................................................................................... 79
       Research, Monitoring and Evaluation Activities ...................................................................... 89
       Needed Future Actions ............................................................................................................. 93
       Actions by Others ..................................................................................................................... 94

Appendix A. Creston Hatchery HGMP (separate document)
Appendix B. Color Plates (separate document)

List of Figures
Figure 1. U.S. portion of the Flathead River Subbasin ...................................................................... 2
Figure 2. Annual Discharge of the Flathead River Subbasin in acre-feet .......................................... 4
Figure 3. Land Uses in the Flathead River Subbasin ......................................................................... 5
Figure 4. Landownership in the U.S. portion of the Flathead River Subbasin .................................. 7

List of Tables
Table 1. Population of major Flathead Subbasin Counties, 1980-1997 ............................................. 6
Table 2. Flathead River Subbasin National Wild and Scenic Rivers ................................................. 8
Table 3. North Fork Flathead Snorkel/Petersen population estimates (95 percent confluence
      interval) by section for westslope cutthroat trout .................................................................... 10
Table 4. Middle Fork Flathead River Snorkel/Petersen population estimates (95 percent confidence
      interval) by section for westslope cutthroat trout .................................................................... 11
Table 5. South Fork Flathead River Snorkel/Petersen population estimates (95 percent confidence
      intervals) by section for westslope cutthroat trout ................................................................... 12
Table 6. Catch data for westslope cutthroat trout collected by MFWP personnel in sections of the
      South Fork Flathead River ....................................................................................................... 12
Table 7. Summary of South Fork Flathead bull trout spawning site inventories from 1993-1998 in
      the annual index sections ......................................................................................................... 13



Flathead Subbasin Summary                                                        ii                                                                    3/6/01
Table 8. Mean catch per unit effort (CPUE) for rainbow, westslope cutthroat, and bull trout, night
     electrofishing on Flathead River in February and March, 1997 and 1998 .............................. 14
Table 9. List of native and non-native fish species in Flathead Lake .............................................. 15
Table 10. Percent species composition of fish caught in gill nets in Flathead Lake, annual spring
     monitoring series, 1981-1998 .................................................................................................. 16
Table 11. Flathead River, May 1998 electrofishing summary ......................................................... 17
Table 12. Flathead River, October 1998 electrofishing summary .................................................... 17
Table 13. Jocko River 1998 electrofishing summary ....................................................................... 18
Table 14. Crow Creek 1998 electrofishing summary ....................................................................... 18
Table 15. Flathead Subbasin target mammal species ....................................................................... 19
Table 16. Bird species in the subbasin considered a high priority for conservation ........................ 20
Table 17. Sensitive species ............................................................................................................... 22
Table 18. Acres of wildlife habitat lost to hydroelectric development, mitigation accomplished
     through July 2000, and mitigation remaining .......................................................................... 42
Table 19. Flathead River Subbasin land ownership ......................................................................... 49
Table 20. Flathead River Subbasin Summary FY 2002 - 2004 BPA Funding Proposal Matrix .... 126




Flathead Subbasin Summary                                            iii                                                         3/6/01
Flathead River Subbasin Summary
           Subbasin Description

           General Description
           Subbasin Location
The Flathead Subbasin, located in northwestern Montana and the southeastern corner of
British Columbia, constitutes the northeastern-most drainage of the Columbia River.
Tributaries originate in Glacier National Park, the Bob Marshall Wilderness, and Canada.
The mouth of the river is located at Paradise, Montana. East to west, the subbasin stretches
141 km (88 miles), north to south, 281 km (175 miles) (Figure 1).

           Drainage Area
The Flathead River Subbasin encompasses almost six million acres. The upper mainstem
of the Flathead River begins where the North, Middle, and South Forks merge near the
town of Columbia Falls (elevation 3,100 feet). The Whitefish and Stillwater Rivers, which
drain the northwest part of the basin, join the upper Flathead River below Kalispell. Near
Holt, the river empties into Flathead Lake. At the town of Big Fork, the Swan River flows
into Flathead Lake. The lower Flathead River leaves Flathead Lake at the lake's southwest
corner and flows 116 km (72 miles) south and west to its confluence with the Clark Fork of
the Columbia River (elevation 2,500 feet). The lower Flathead River's primary tributaries
are the Little Bitterroot and Jocko Rivers and Crow, Mission, and Camas Creeks.

           Climate
The climate of the Flathead River Subbasin is strongly influenced by pacific maritime
airmasses. In winter, moist air dominates, often shrouding the basin with low-lying, gray
clouds and bringing mild temperatures. Kalispell, for example, has a mean January
temperature of 20°F. Occasionally, continental airmasses composed of arctic or polar air
spill over the Continental Divide, bringing clear skies and frigid temperatures (-20°F or
colder) (Zackheim 1983; Cunningham 1982).
        Pacific airmasses usually dominate during the spring and early summer as well.
They bring partly cloudy conditions, punctuated by rain and occasional warm, dry periods.
In July, a high-pressure system often moves over the subbasin. Skies clear and
temperatures range from the 70s to the high 90s with occasional, short, hotter periods.
Afternoon thunderstorms are common throughout the summer. Fall repeats the unsettled
weather pattern of spring; clear skies alternate with periodic cloudy weather (Zackheim
1983).




Flathead Subbasin Summary                    1                                      3/6/01
Figure 1. U.S. portion of the Flathead River Subbasin


Flathead Subbasin Summary                   2           3/6/01
        The varying topography of the Flathead River basin results in extreme local
fluctuations in precipitation. The mountains receive between 80 and 120 inches of
precipitation annually, mostly in the form of snow (Finklin 1986). Mountain ridges have
snowpacks of up to 20 feet or more. Valleys annually receive an average of between 15 and
20 inches of precipitation. The rainiest months occur in May and June (Finklin 1986).
Winter snowfalls seldom exceed six inches at a time in the valleys; frequent winter thaws
usually keep total valley snow cover at under a foot.

           Topography
The east half of the subbasin, which is bordered by the Continental Divide, is broken by a
series of rugged mountain ranges, chief among them the Whitefish, Swan, Mission,
Livingstone, and Flathead Ranges. Their ridges generally trend northwest to southeast;
their highest peaks reach 8,000 to 10,000 feet. The west half of the subbasin is quite
different topographically. It is basically a 160-km-long oval depression interspersed with
groups of rolling hills. The north half of this depression is dominated by the upper Flathead
River Valley, the south half by the Mission, Jocko, Little Bitterroot, Camas Prairie, and
Lower Flathead valleys. Flathead Lake, with a surface area of 126,000 acres, lies at the
depression's center.

           Geology
The Flathead River Subbasin is situated along the west limb of the Rocky Mountains.
Precambrian rocks of the Belt Supergroup form the bedrock under virtually the entire
subbasin. Belt rocks are exposed in the mountain ranges, as well as in many of the lower
hills of the valleys. The major rock types include argillite, siltite, quartzite, and limestone.
Almost all of the forested acres are underlain by these Precambrian rocks, which are fine
grained, moderately metamorphosed sediments deposited over one billion years ago. Belt
sediments are highly stable (they have low erosion potential), and they account for the
generally high stability of the subbasin's watersheds. Igneous rocks also occur but only in a
few areas. Over the last 100,000 years, advances and recessions of glaciers have
extensively modified landscapes. The most recent glacial advance receded about 10,000
years ago and left unconsolidated surface sediments in many watersheds that include
glacial tills, glacial stream deposits, and fine grained sediments deposited in Glacial Lake
Missoula. (CSKT 2000).

           Hydrology
In terms of volume, the Flathead River is Montana's fourth largest river (Zackheim 1983).
The mean annual discharge of the river system is nine million acre-feet (Figure 2,
Zackheim 1983). The flow rate for the lower Flathead River averages over 12,000 cubic
feet per second (cfs). The three forks of the Flathead together supply about 80 percent of
the water carried within the system. Flows on the North Fork average about 3,000 cfs near
Columbia Falls, approximately the same as the flows on the Middle Fork. On both, peak
spring runoff often exceeds 10 times the average flow (Zackheim 1983). The North and
Middle forks experience an average elevation drop of 26 and 15 feet per mile, respectively.



Flathead Subbasin Summary                      3                                        3/6/01
On the South Fork, the average annual discharge into Hungry Horse Reservoir is 2,300 cfs
(Deleray 1999).




Figure 2. Annual Discharge of the Flathead River Subbasin in acre-feet

        The Whitefish and Stillwater rivers merge just southeast of Kalispell and contribute
about five percent of the flow of the upper Flathead. The Swan River provides about one
tenth of the water flowing into Flathead Lake. The largest tributary of the lower Flathead is
the Jocko River, but it contributes less than four percent of the total flow volume
(Zackheim 1983).
        Flathead Lake has a surface area of roughly 197 square miles, a mean depth of 164
feet, and a maximum depth of 370 feet. It is the largest natural freshwater lake in the
western U.S. The lake is classified as oligomesotrophic (Zackheim 1983).
        The lower Flathead River is a low-gradient river (3.4 ft/mile) draining a 954,313-
acre watershed. With the exception of the first 11.26 km of the river, which flow through a
steep canyon, the lower Flathead River is a comparatively smooth-flowing, shallow river in
which riffle and pool areas blend. Approximately 94 percent of the river's 116-km length
fall within the Flathead Indian Reservation.
        The basin is nearly completely underlain with Precambrian sedimentary rock, which
is characteristically deficient of nutrients. As a result, the water is likewise nutrient poor
and flows distinctly clear.




Flathead Subbasin Summary                     4                                      3/6/01
             Soils
Soils formed from residual and colluvial materials eroded from Belt rocks or in materials
deposited by glaciers, lakes, streams, and wind. Wind deposits include volcanic ash from
Cascade Range volcanoes in Washington and Oregon.
        Since glacial recession, geologic conditions have been relatively stable. This is
suggested by the widespread distribution of 6,700-year-old Mt. Mazama volcanic ash in
forested drainages, well developed soil profiles on many glacial features, stable stream
channels, and stable slopes in forested watersheds. The volcanic ashes produce soils with
very high soil-moisture holding capacity, high fertility, low strength, and high erodability.
        In many areas, soils formed in glacial till and are generally loamy, with moderate to
high quantities of boulders, cobbles, and gravels. Although soils within the mountainous
regions vary widely in character, most mountain and foothill soils are on steep slopes and
are well drained with large amounts of broken rock. Rock outcrops are common.
        Soils deposited by glaciers or flowing water cover about 40 percent of the national
forest lands. These are, for the most part, deep, well-drained, and productive soils. About
15 percent of the national forest lands have soils that developed in place through
weathering of bedrock. Most of forest soils in the subbasin are somewhat resistant to
erosion by water. In most of the valleys, soils are deep, relatively productive, and gently
sloping (CSKT 2000; Zackheim 1983).

             Land Uses
Within the subbasin, the upper Flathead River Valley and the Mission Valley are the areas
that have been the most extensively developed for agricultural and urban uses. Additional
important agricultural areas include the Jocko and Little Bitterroot valleys. The low-
elevation treeless slopes in the southwestern corner of the basin provide significant
rangeland, while forests dominate the mountainous terrain, which composes the vast
majority of the basin area. Major land uses are summarized in Figure 3 (Zackheim 1983).
Table 1 summarizes population trends in the three major counties. Figure 4 shows land
ownership in the U.S. portion of the subbasin.

Forest and Alpine Area
           Rangeland
             Cropland
                Wat er
          Urban Land

                         0   10   20   30 40 50 60 70 80       90 100
                                        Percent of Land Area

Figure 3. Land Uses in the Flathead River Subbasin




Flathead Subbasin Summary                        5                                   3/6/01
Table 1. Population of major Flathead Subbasin Counties, 1980-1997
 County      1980 Population     1997 Population     Area (sq. mi.)   People/sq. mi.
 Flathead         51,966              71,707             5,099             14.1
 Lake             19,056              25,341             1,494               17
 Sanders           8,675              10,253             2,762              3.7
 Totals           79,697             107,301             9,355           13.5 (Ave.)


            Impoundments and Irrigation Projects
Hungry Horse Dam, completed in 1952, is located 8.4 km upstream from the confluence of
the South Fork and the mainstem of the Flathead River. Hungry Horse Reservoir is 56 km
long and covers 23,782 acres at full pool. The dam, operated by the Bureau of Reclamation
(BOR), provides flood control, electrical power production, and water storage capability
for the Columbia River system. Annual operations for power and flood control result in a
reservoir draft toward minimum pool by mid-April and refill toward full pool (elevation
3,560 feet) during July. The maximum reservoir drawdown on record was 188 feet. Hungry
Horse Dam has a peak capacity of 320,000 kilowatts. Kerr Dam, located 6.9 km
downstream of the natural lake outlet, was built in 1938 and is currently operated by
Pennsylvania Power and Light Montana (PPLM). The dam regulates the top three meters of
water and is operated to provide flood control and power production. Its peak capacity is
180,000 kilowatts. The dam is now operated as a base-load facility. Presently, flood control
and recreation require the lake level to be dropped to the low pool elevation of 2,883 feet
by April 15, refilled to 2,890 feet by May 30, raised to full pool elevation of 2,893 feet by
June 15, and held at full pool through Labor Day (Deleray et al. 1999). Bigfork Dam is a
small hydroelectric facility with a 4,000-kilowatt peak capacity. It is located on the Swan
River less than 2 km from Flathead Lake.
        On the Flathead Indian Reservation, the Flathead Agency Irrigation District (FAID)
consists of an intricate network of natural channels, irrigation canals, and storage reservoirs
that retain spring runoff and distribute the water to cultivated lands. Approximately 1,930
km of irrigation canals and 17 reservoirs exist under FAID. The larger FAID reservoirs
include Pablo, Ninepipe, Crow, Kicking Horse, and Hubbard. Several natural lakes on the
Flathead Indian Reservation have been adapted for controlled irrigation releases. An
unquantified number of secretarial water rights also exist throughout the basin.




Flathead Subbasin Summary                     6                                        3/6/01
Figure 4. Landownership in the U.S. portion of the Flathead River Subbasin



Flathead Subbasin Summary                   7                                3/6/01
             Protected Areas
In the U.S. part of the subbasin, approximately 1.9 million acres have significant protective
status and 338 km of river are classified as wild, scenic or recreational (Table 2, Zackheim
1983). In Canada, Akamina-Kishinna Provincial Park is located adjacent to the northern
edge of Glacier Park.

Table 2. Flathead River Subbasin National Wild and Scenic Rivers
River                                                       KM
North Fork of the Flathead River
   US/Canada Border to Camas Bridge (Scenic)                65.5
   Camas Bridge to Middle Fork (Recreational)               28.3
Middle Fork Flathead River
   Headwaters to Bear Creek (Wild)                          74.9
   Bear Creek to South Fork (Recreational)                  87.0
South Fork Flathead River
   Headwaters to Spotted Bear River (Wild)                  82.5
   Spotted Bear River to Hungry Horse Res. (Recreational)   14.1



             Fish and Wildlife Resources

             Fish and Wildlife Status
             Fish
             Westslope Cutthroat Trout
Westslope cutthroat trout were petitioned for listing under the Endangered Species Act
(ESA), U.S. Fish and Wildlife Service (USFWS 1998). The USFWS determined that
listing is not warranted at this time. In Montana, the species has been designated a Species
of Special Concern. Westslope cutthroat trout populations above Hungry Horse Dam form
one of the strongest, most secure metapopulations of westslope cutthroat trout in existence
(Marotz, MDFW&P, pers. com. 2000). Below the dam, cutthroat numbers have declined
due to loss of habitat and negative interactions with non-native fish species (e.g.
hybridization with rainbow trout and predation by lake trout).

             Bull Trout
Bull trout were listed in 1998 as a threatened species under the ESA. The population in
Hungry Horse Reservoir and its headwaters is arguably the second strongest
metapopulation in existence (Marotz, MDFW&P, pers. com. 2000). Hungry Horse Dam
isolated bull trout populations above and below the dam. Populations in the reservoir have
stabilized at sustainable numbers, and Montana Fish, Wildlife & Parks (MFWP)
established a comprehensive monitoring program to alert managers to any change in
population status. MDFW&P and the Confederated Salish and Kootenai Tribes (CSKT)
also carefully monitor the bull trout population in the Flathead system below Hungry Horse
Dam. At least 20 disjunct populations have been identified (MBTSG 1995). Results have
documented an alarming reduction in bull trout spawning redds since the early 1990s. The
population declined to the lowest point in the 20-year record during the period from 1992



Flathead Subbasin Summary                               8                            3/6/01
to 1996. During 1997 and 1998, redd counts rebounded somewhat but remain at 50 percent
of the long-term average.
        Six distinct populations of bull trout occur within the Flathead Reservation (Hansen
and DosSantos 1997). These populations occur in the lower Flathead River and the Jocko
River and Mission Creek watersheds.

           Native Trout and Char Life Histories in the Subbasin
The native trout and char—westslope cutthroat trout and bull trout—have evolved varied
life histories to be successful in the Flathead drainage. There are three life history forms:
(1) adfluvial stocks, which spawn and rear in river tributaries and move downstream to
mature and reside in Flathead Lake; (2) fluvial stocks, which spawn and rear in river
tributaries then move downstream to mature and reside in the Flathead River, and; (3)
tributary or ―resident‖ stocks, which spawn, rear, and reside for their entire life cycle in a
tributary stream (Shepard et al. 1984, Fraley and Shepard 1989, Liknes and Graham 1988).
Westslope cutthroat trout employ all three of these strategies in the Flathead system. Bull
trout are primarily adfluvial, although recent radio telemetry results have documented a
fluvial component (Muhlfeld et al. 2000), and individual fish may combine the two
strategies. Juveniles reside in tributaries for one to three years before migrating
downstream into river or lake habitats (Shepard et al. 1984). Adfluvial fish take advantage
of improved forage and growth rates during lake residence and thus reach larger sizes than
either fluvial or tributary residents. Tributary fish mature at relatively smaller sizes (~200
mm) and don’t grow as large (>400 mm) as fish using the other strategies (Shepard et al.
1984, Liknes and Graham 1988).
         These three life history forms inhabit three general types of habitat: tributary
streams, mainstem river and forks, and lake. In order for fish populations in the basin to be
successful, all habitats must present adequate conditions for fish survival at related life
history stages. Degraded conditions in one of these habitat types may limit the population.

           Geographical Summary
The relative abundance of bull trout and the genetic purity of westslope cutthroat trout in
the upper part of the subbasin are shown on Plates 1 through 10 in Appendix B.

           Three Forks of the Flathead
Westslope cutthroat trout, bull trout, and mountain whitefish are the native gamefish
species found in the South, Middle, and North forks of the Flathead River and their
tributaries. Adfluvial cutthroat trout generally occur in the lower South Fork of the
Flathead up to Meadow Creek Gorge and in the Middle and North forks of the Flathead
River. Fluvial westslope cutthroat trout are found primarily in the mainstem of the South
Fork above Meadow Creek Gorge, and portions of the Middle Fork. The resident form of
westslope cutthroat trout completes its entire life cycle solely in headwater tributaries to all
three Flathead River forks (Deleray 1999).

        Bull trout appear to be primarily adfluvial in the three forks of the Flathead River.
At this time, MFWP biologists have not observed evidence of fish residence in tributaries



Flathead Subbasin Summary                         9                                     3/6/01
for complete life cycles. They have observed all age classes during summer river surveys,
which may be evidence of a fluvial component.

                                      North Fork of the Flathead River
Results from three years of population estimates for the Ford section of the North Fork are
summarized in Table 3 (Deleray 1999). From 1990 to 1996, overall cutthroat trout numbers
dropped dramatically from 282 to 96 per kilometer. The majority of the decline occurred in
the small cutthroat trout with mid- and large-size fish maintaining low numbers in all three
years. It is probably that all three life history forms (resident, fluvial, and adfluvial) of
cutthroat trout exist in the North Fork and its tributaries.

Table 3. North Fork Flathead Snorkel/Petersen population estimates (95 percent confluence
interval) by section for westslope cutthroat trout
                                            Number of Fish Per Kilometer
    Date        <254 mm (10")         254-305 mm (10-12")     >305 mm (12")   All Fish Combined
   8/3/90         411 (+/-79)               16 (+/-17)             0             428 (+/-82)
  8/18/93         232 (+/-44)                15 (+/-9)          1 (+/-1)         249 (+/-46)
  8/30/96*        133 (+/-30)                10 (+/-5)          3 (+/-2)         146 (+/-31)
*Approximately half of previous marking effort.


        Bull trout core areas in the North Fork Flathead River drainage are Big, Coal,
Whale, Trail, Red Meadow, Howell, and Cabin Creek drainages. The North Fork itself is a
nodal habitat (nodal habitats are those that provide a migratory corridor, overwintering
area, or are otherwise critical to the population at some stage of its life cycle (MBTSG
1995a)).

                                     Middle Fork of the Flathead River
Estimates conducted in the Middle Fork Flathead River are summarized in Table 4. In the
uppermost (Gooseberry) section, there has been an increasing trend in total cutthroat trout
abundance when comparing 1988, 1991, and 1994. Cutthroat trout in the upper reaches are
primarily resident fish, spending their entire life in or near the survey section (Deleray
1999). Two estimates were conducted in the Schafer Section (1988 and 1994). The
estimated number of small cutthroat trout increased dramatically from 37 per kilometer in
1988 to 148 per kilometer in 1994. (Deleray 1999). Estimates have been conducted for two
years (1997 and 1998) in the Spruce Park section. A higher proportion of larger fish was
present in this section than in upstream sections (Deleray 1999). Estimates in the Paola
Section were conducted annually from 1995 through 1997 to establish a baseline data set.
Abundance of small cutthroat trout in the Paola section appeared to increase steadily over
the three years (Deleray 1999).
        Cutthroat trout below the Schafer section appear more migratory in nature than
those in above sections, suggesting the presence of all three life history forms within the
Middle Fork. Lake McDonald appears to be utilized by some Middle Fork cutthroat trout.
Graham (1980) documented cutthroat trout migrating upstream from Flathead Lake into the
Middle Fork as well (Deleray 1999).



Flathead Subbasin Summary                                10                                    3/6/01
Table 4. Middle Fork Flathead River Snorkel/Petersen population estimates (95 percent
confidence interval) by section for westslope cutthroat trout
                                                Number of Fish Per Kilometer
 Section                                                                              All Fish
 (Length)         Date      <254 mm (10")    254-305 mm (10-12")     >305 mm (12")   Combined
 Gooseberry      7/20/88       72 (+/-20)          4 (+/-3)              1 (+/-0)     77 (+/-20)
 (3 km)          7/29/91       98 (+/-27)          4 (+/-1)              1 (+/-0)    102 (+/-23)
                 7/18/94      125 (+/-54)          1 (+/-1)              1 (+/-0)    127 (+/-50)
 Schafer         7/20/88        37 (+/-3)             0                     0          37 (+/-3)
 (3 km)          8/9/94*          148                 3                     1            152
 Spruce Park     8/13/97      150 (+/-29)         56 (+/-17)            14 (+/-5)    219 (+/-33)
 (3.6 km)        8/12/98       59 (+/-12)          21 (+/-8)            14 (+/-5)     94 (+/-16)
 Paola           8/31/95        16 (+/-8)          14 (+/-5)             8 (+/-4)     38 (+/-10)
 (3.2 km)        8/21/96       54 (+/-16)          12 (+/-5)             4 (+/-2)     70 (+/-16)
                 8/20/97       73 (+/-40)          14 (+/-5)             5 (+/-4)     92 (+/-31)


       Bull trout core areas in the Middle Fork Flathead River are Nyack, Park, Ole, Bear,
Long, Granite, Morrison, Schafer, Clack, Strawberry, and Bowl Creek drainages. The
Middle Fork Flathead River is a nodal habitat for bull trout.

                              South Fork of the Flathead River
Beginning in the uppermost (Gordon) section of the South Fork, MFWP conducted
estimates in 1984 and 1987 (Table 5). Estimates combining all fish were quite similar
between the two years. Large cutthroat trout tend to reside in this portion of the South Fork
at least until fall and then seek preferred habitat for overwintering. Mean lengths and catch
rates were consistently the highest in the Youngs and Danaher Creeks confluence area and
in the Gordon section when compared to other South Fork sections and streams (Table 6).
         The Black Bear Section consistently contained the highest estimated number of
cutthroat trout per kilometer of the South Fork sections (Deleray 1999). Estimated
cutthroat trout numbers in the Harrison Section were generally lower than in the Black
Bear Section (Table 5). Research suggests that cutthroat trout above Meadow Creek Gorge
are generally a separate population with a fluvial life history, while cutthroat trout below
the Gorge are both fluvial and adfluvial fish, some utilizing Hungry Horse Reservoir
(Deleray 1999).




Flathead Subbasin Summary                    11                                      3/6/01
Table 5. South Fork Flathead River Snorkel/Petersen population estimates (95 percent
confidence intervals) by section for westslope cutthroat trout
                                                         Number of Fish Per Kilometer
 Section                                                                                            All Fish
 (Length)      Date        <254 mm (10")             254-305 mm (10-12")     >305 mm (12")         Combined
 Gordon        1984*             No Estimate             No Estimate           No Estimate         206 (+/-62)
 (2.2 km)     8/13/87                85                 98 (>254 only)         No Estimate         183 (+/-37)
 Black Bear   8/28/83        494 (+/-190)                 105 (+/-85)           42 (+/-34)         641 (+/-220)
 (4.4 km)      8/7/85        419 (+/-177)                  56 (+/-27)           39 (+/-31)         514 (+/-164)
              7/21/89         309 (+/-79)                  42 (+/-20)           31 (+/-11)          381 (+/-74)
               7/2/92         325 (+/-82)                 151 (+/-42)           51 (+/-12)          527 (+/-78)
              7/28/95         339 (+/-75)                  60 (+/-29)           32 (+/-14)          431 (+/-81)
              7/23/98         232 (+/-40)                  81 (+/-22)            33 (+/-9)          346 (+/-46)
 Harrison      8/9/84        267 (+/-100)                  15 (+/-11)             4 (+/-4)         285 (+/-102)
 (2.2 km)     8/23/85         186 (+/-48)                  26 (+/-11)          No Estimate          213 (+/-47)
              7/30/90         207 (+/-37)                  34 (+/-22)            16 (+/-7)          257 (+/-42)
              8/20/93         189 (+/-57)                  62 (+/-18)            17 (+/-8)          268 (+/-53)
              8/15/96         443 (+/-87)                   19 (+/-9)            13 (+/-6)          475 (+/-82)


Table 6. Catch data for westslope cutthroat trout collected by MFWP personnel in sections
of the South Fork Flathead River
                                                       Mean                  Percent     Percent
                                                      Length       Range    >254 mm     >305 mm       Catch Rate
   Section          Area              Year     N       (mm)        (mm)       (10")       (12")       (Fish/Hr.)
 Gordon       Murphy Flats            1960      80      228       90-406       34            11          N/A
              L. Salmon Cr.           1981     151      230       110-350      26             8           3.7
              B. Salmon Cr.           1984      92      240       170-370      46            18          N/A
              B. Salmon Cr.           1985     296      258       150-400      59            24           7.0
              Youngs/Danaher          1985     111      255       120-340      42            23           7.7
              Independence Pk.        1986     586      274       120-427      61            31           8.7
              Youngs/Danaher          1986     142      268       190-425      42            24           8.8
              Gordon                  1987      15      272       218-378      60            20           1.3
              Youngs/Danaher          1987     137      264       165-400      56            20           7.7
              Youngs/Danaher          1988     106      243       179-452      28            12           6.0
              Youngs/Danaher          1989     145      244       160-443      38            11           9.7
              Youngs/Danaher          1990     133      263       140-446      53            20           9.2
              Youngs/Danaher          1991     100      266       155-442      53            23           8.5
              Youngs/Danaher          1992     132      272       180-442      59            23          11.0
              Youngs/Danaher          1993     101      277       200-440      61            24           7.8
              Youngs/Danaher          1994     104      289       170-445      63            40           8.3
              Youngs/Danaher          1995      90      274       170-431      57            28           5.1
              Youngs/Danaher          1996      48      265       165-470      31            27           4.6
 Black Bear   Mid Cr.                 1983     112      213       160-378       8             2          N/A
              Black Bear              1985     595      228       117-401      28             8          6.3
              Black Bear              1986      54      231       101-421      26            13          N/A
              Black Bear              1987      38      274       203-381      61            26          1.7
              Black Bear              1989     428      215       120-430      24            11          4.1
              Black Bear              1992     477      239       109-440      38            13          5.2
              Black Bear              1995     329      219       112-404      19             8          4.1
              Black Bear              1998     432      220       112-401      32            10          4.6




Flathead Subbasin Summary                                12                                           3/6/01
                                                                  Mean                        Percent      Percent
                                                                 Length       Range          >254 mm      >305 mm         Catch Rate
      Section           Area              Year        N           (mm)        (mm)             (10")        (12")         (Fish/Hr.)
   Harrison       Harrison                1984        153         197         112-238           10              2            1.7
                  Harrison                1985        142         212         152-343           13              0            2.4
                  Harrison                1987         31         241         157-358           25             16            3.8
                  Harrison                1989         90         198         123-396           10              6            3.8
                  Harrison                1990        208         216         135-390           14              7            5.7
                  Harrison                1993        151         230         136-352           34              7            2.2
                  Harrison                1996        287         188         124-420            8              3            4.9


          Over the initial four years of redd counts, field crews observed an average of 280
  bull trout redds in our annual monitoring sections. The 1997 total of 269 is 4 percent below
  this average figure (Deleray 1999). Data are summarized in Table 7.

  Table 7. Summary of South Fork Flathead bull trout spawning site inventories from 1993-
  1998 in the annual index sections
Reservoir Tributaries                                                        Upper River Tributaries
                1993    1994      1995     1996        1997        1998                        1993     1994    1995      1996     1997
Wounded Buck       22        29     34           41         14           5   Youngs              40       24         34      74         43
Wheeler           12         10      1         3             1           4   Gordon              35       44         46      58         30
Sullivan          25          8      --       52            50          54   White River         39       60         45      86         31
Quintonkin         5          3      7         4             0          11   Little Salmon       56       47         43     134        100
Totals            64         50     42       100            65          74   Totals             170      175        168     353        204



                Mainstem of the Flathead River upstream of Flathead Lake
  Salmonids using the mainstem of the Flathead River have diverse life history strategies,
  which makes it difficult to assess the status of populations. Mountain whitefish, westslope
  cutthroat trout, and bull trout have both fluvial and adfluvial life histories, while rainbow
  trout appear to be primarily fluvial. Within a species, individual fish of one life history are
  generally not visually distinguishable from those of another life history. Determining
  population status for these species is difficult due to the timing of seasonal migrations and
  overlapping habitat use by the different life histories.
          Adfluvial westslope cutthroat trout use the mainstem river and North and Middle
  Forks as a migratory corridor. Adults migrate to and from spawning tributaries from early
  winter through summer, while juveniles migrate from rearing streams toward the lake from
  early summer through winter (Shepard et al. 1984, Liknes and Graham 1988). Similarly,
  juvenile bull trout emigrate from tributaries to the Flathead River and Lake system from
  early summer through winter. In early summer (April to July), adult adfluvial bull trout
  migrate from the lake into the river and move toward staging areas. They then move into
  spawning tributaries generally in August, and following spawning in September, move
  rapidly back downstream to Flathead Lake (Shepard et al. 1984). Adult mountain whitefish
  also make spawning migrations as the fall spawning period approaches, and rainbow trout
  adults move in response to spring spawning. Thus, at any time of the year, different
  salmonids, life histories, and age groups are migrating throughout the river system.



  Flathead Subbasin Summary                                        13                                                     3/6/01
        A recent investigation found the mountain whitefish to be the most numerous
species (hundreds per night) in both river sections (Deleray et al. 1999). Investigators also
observed but did not enumerate largescale suckers. They captured rainbow trout, westslope
cutthroat trout, bull trout, lake trout, brook trout, and lake whitefish. Rainbow, westslope
cutthroat trout, and bull trout dominated the trout and char catch. Future surveys are needed
to assess trends in population abundances and to relate variation in catch to river discharge,
water temperature, or other factors.
        Hybridization between rainbow and westslope cutthroat trout is prevalent in the
upper Flathead River. The concentration of hybrid trout appears higher in the Columbia
Falls section than in the Kalispell section.

Table 8. Mean catch per unit effort (CPUE) for rainbow, westslope cutthroat, and bull
trout, night electrofishing on Flathead River in February and March, 1997 and 1998
Kalispell Section                Rainbow            Westslope Cutthroat            Bull Trout
 Year      CPUE      All Sizes     >300    <300     All    >300   <300     All Sizes   >400     <400
                                    mm     mm      Sizes   mm      mm                  mm       mm
 1997         #/hr        3.1       2.2     1.0      2.7    2.0     0.6      1.5        0.4      1.1
 1998         #/hr        6.1       1.8     4.3    18.9     8.8    10.1      3.5        0.3      3.2
 1981      #/km/hr        0.5       ---      ---     4.2    2.1      ---     ---        ---      0.4
 1997      #/km/hr        1.1       0.7     0.3      0.9    0.7     0.2      0.5        0.1      0.4
 1998      #/km/hr        2.1       0.6     1.4      6.4    3.0     3.4      1.2        0.1      1.1
Columbia Falls Section
 1997         #/hr       17.9       7.2    10.8     4.5    2.6      1.9      2.2       0.6       1.6
 1998         #/hr       21.3       7.6    13.7     3.0    0.8      2.2      2.7       0.9       1.8
 1981      #/km/hr        2.5       ---      ---    3.0    2.8       ---     ---       ---       ---
 1997      #/km/hr        9.0       3.6     5.4     2.3    1.3      1.0      1.1       0.3       0.8
 1998      #/km/hr       10.7       3.8     6.9     1.5    0.4      1.1      1.4       0.5       0.9



             Flathead Lake
From a fish community perspective, Flathead Lake has supported three very different
species assemblages. Prior to settlement by Europeans, the fish community was solely
comprised of native species, which colonized the waters following the last glacial period,
roughly 10,000 years ago. Bull trout, westslope cutthroat trout, and mountain and pygmy
whitefish were the only salmonids. Bull trout and northern pikeminnow were the dominant
piscivorous fishes. Most likely, the minnows (n. pikeminnow and peamouth) dominated in
fish abundance and biomass (Elrod, et al. 1929). Accurate depiction of relative species
abundance is difficult due to a lack of recorded and quantified surveys or fishery
encounters.
       Europeans arrived in the mid-1880s, and beginning in the early 1900s introduced a
number of other fish species (Table 9, Hanzel 1969, Alvord 1991) (Hanzel 1969; Alvord
1991). By the 1920s, a new fish community had established itself with abundant kokanee,
lake trout, lake whitefish, and yellow perch in addition to the native species. Kokanee and
yellow perch dominated the recreational fishery. Angler creel surveys in 1962, 1981, and
1985 show kokanee provided the majority of the sport fishery—from 77 to 97 percent of




Flathead Subbasin Summary                          14                                           3/6/01
harvested fish numbers (Evarts 1998). This new community was relatively stable until the
mid-1980s.

Table 9. List of native and non-native fish species in Flathead Lake
 Native                      Non-Native                 Date Introduced
 Bull Trout                  Lake Trout                 1905
 Westslope Cutthroat Trout   Lake Whitefish             1890
 Mountain Whitefish          Kokanee                    1916
 Pygmy Whitefish             Yellow Perch               1910
 Longnose Sucker             Northern Pike              1960's (Illegally)
 Largescale Sucker           Rainbow                    1914
 Northern Pikeminnow         Brook Trout                1913
 Peamouth Chub               Largemouth Bass            1898
 Redside Shiner              Pumpkinseed Sunfish        1910
 Sculpins                    Black Bullhead             1910


        Beginning in 1968, MFWP introduced opossum shrimp (Mysis) into Ashley, Swan,
Tally, and Whitefish lakes in the Flathead Lake drainage. Mysis moved out of these lakes
and downstream into Flathead Lake, where they were first collected in 1981. By the mid-
1980s, mysis established an abundant population and caused the third shift in the fish
assemblage in Flathead Lake.
        Following their first collection in Flathead Lake in 1981, the mysis population
                                                           2                         2
increased exponentially from under three mysis/m in 1984 to a peak of 130 mysis/m in
1986 (Beattie and Clancey 1991, Spencer et al. 1991). Mysis density then dropped below
     2                                                                2
60/m by 1988 and has since varied between 16 and 68/m (Spencer et al. 1991, Beattie and
Clancey 1991, Flathead Basin Commission 1993, Stanford et al. 1997). This created
unforeseen and far-reaching changes in the Flathead Lake system due to unique feeding
behavior of mysis. Mysis became a competitor with fish species dependent on the
zooplankton forage base. It also provided an abundant food source for benthic fishes, such
as lake trout and lake whitefish, and substantially increased survival, recruitment, and
abundance of these species.
        Table 10 shows how the fish population has changed since the introduction of
mysis. Percent species composition has changed dramatically. For gillnet surveys, sample
years 1981 and 1983 describe the pre-mysis fish community and provide baseline fishery
information for comparison to current populations. In the sinking nets, there was a shift in
species composition from numerical dominance by peamouth (pre-mysis) to lake whitefish
(post-mysis). In 1981 and 1983, peamouth comprised about 40 percent of catch
composition, while lake whitefish comprised only about 15 percent. In recent catches, lake
whitefish comprised roughly 75 percent of the catch. One of the more dramatic
transformations has been in the relative abundance of bull trout and lake trout. In 1981 and
1983, bull trout numbers comprised 10 and 13 percent of fish caught in sinking nets, while
lake trout numbers comprised only 0.2 and 0.9 percent, respectively. Since 1996, bull trout
comprised roughly one percent, while lake trout comprised six to 14 percent of gillnet
catch. Similar declines have been observed in mountain whitefish in sinking net catch.




Flathead Subbasin Summary                          15                               3/6/01
 Mountain whitefish comprised roughly four percent of catch composition in the early
 1980s and now have a very low incidence (<1 percent).
         Westslope cutthroat trout showed the greatest declines in floating net catches. In the
 early 1980s, westslope cutthroat trout made up 20 to 40 percent of the catch, while in
 recent years they composed less than 20 percent. With the exception of lake trout and
 northern pikeminnow, the other species have not shown obvious changes in percent
 composition.

 Table 10. Percent species composition of fish caught in gill nets in Flathead Lake, annual
 spring monitoring series, 1981-1998
                                                            Percent Species Composition
          # of    Total #
 Year     Nets    of Fish   WCT      BT     LT     LWF       MWF       KOK      NSQ       PM     LNSU      CSU    YP
 Sinking Nets
 1981      23      450         0.4   13.3    0.2     16.2     4.4       2.2       15.6    41.1    3.8       0.9   1.8
 1983      30      459         0.2   10.7    0.9     13.7     4.1       1.1       11.1    39.0    8.1       2.2   8.7
 1992      18      369         0.0    2.4    8.4     55.8     0.3       0.0       12.7    15.7    1.9       1.1   1.6
 1993      18      299         0.7    0.7    8.7     46.2     0.3       0.0       24.1    10.4    4.7       3.3   0.7
 1994      18      555         0.0    0.7   10.1     49.9     0.0       0.0        9.5    26.5    2.5       0.2   0.5
 1995      24      304         0.0    0.3    9.2     54.9     0.0       0.0       15.5    13.5    2.6       2.0   2.0
 1996      30      286         0.0    0.7   13.6     74.8     0.0       0.0        6.6     2.1    1.7       0.3   0.0
 1997      30      524         0.0    1.4   10.3     74.7     0.0       0.0       11.1     0.4    1.4       0.6   0.0
 1998      30      633         0.2    0.6    6.3     74.9     0.2       0.0       12.8     2.1    2.1       0.0   0.9
 Floating Nets
 1981      30      232        43.5   10.9    0.0      1.7     8.7       2.6       14.8    17.8    0.0       0.0   0.0
 1983      30      268        22.8    7.1    0.0      2.6     2.6       4.9       11.9    46.3    0.7       1.1   0.0
 1992      28      149        38.9    3.4   10.1      8.7     6.0       0.0        8.1    22.1    0.7       0.0   0.7
 1993      28      102         9.8    0.0    6.9     19.6     1.0       0.0       37.3    20.6    0.0       3.9   0.0
 1994      30      116        16.4    4.3    8.6      7.8     0.9       0.0       23.3    37.9    0.0       0.0   0.9
 1995      24      51         13.7    2.0    7.8     21.6     0.0       0.0       31.4    17.6    2.0       3.9   0.0
 1996      30      41         17.1   17.1   12.2      2.4     4.9       0.0       19.5    26.8    0.0       0.0   0.0
 1997      30      134        11.2    8.2    4.5      2.2     3.0       0.0       37.3    23.9    0.7       8.2   0.0
 1998      30      608         4.3    2.1    1.5      4.1     0.5       0.2       37.7    46.7    0.0       1.2   0.3
Key: WCT = Westslope Cutthroat, BT = Bull Trout, LT = Lake Trout, LWF = Lake Whitefish, MWF = Mountain Whitefish, KOK
= Kokanee, NSQ = Northern Pikeminnow, PM = Peamouth, LNSU = Longnose Sucker, CSU = Largescale Sucker, YP = Yellow
Perch


         In summarizing the information available on Flathead Lake bull trout, it appears
 that between 1980 and 1991 total estimated bull trout spawner escapement fluctuated
 between 2,000 and 4,000 fish. Limited information from the early 1950s suggests similar
 numbers of spawners at that time. A significant decline in redd numbers occurred during
 the early 1990s due to alteration of the trophic dynamics in Flathead Lake. From 1992 to
 1997, the number of bull trout redds remained relatively stable, but this level was
 approximately 70 percent below the average during the preceding 12-year period (1980-
 1991). Our 1998 count showed an encouraging increase over the previous six years, but it
 was still 50 percent below its pre-mysis levels. The mechanisms causing the decline are not
 completely clear and there remains considerable uncertainty about bull trout ecology and
 trophic interactions in Flathead Lake.



 Flathead Subbasin Summary                            16                                                3/6/01
       Separate bull trout populations occupy the Swan and South Fork Flathead
drainages. Those populations are presently stable or increasing.

             Lower Flathead River and Main Tributaries
The results of 1998 spring and fall electrofishing surveys on the lower Flathead River are
summarized in Table 11 and Table 12.

Table 11. Flathead River, May 1998 electrofishing summary
Species/Lengths                      Mean    Median       SE      SD     Range   Min Max     Count     Percentage
Bull Trout                            374       na         na      na     na     na     na     1          0.5%
Westslope Cutthroat                   326      309        26.1    63.8    171    272   443      6         2.8%
Rainbow-Cut Hybrid                    345       na         na      na      na     na    na      1         0.5%
Rainbow Trout                         345      356        17.5    85.7    281    187   468     24        11.3%
Brown Trout                           404      416         9.9    88.6    385    185   570     80        38.0%
Mountain Whitefish                    142      130         7.5    32.6    145    120   265     19         8.9%
Northern Pike                         566      525        24.9   119.3    429    356   785     23        10.8%
Yellow Perch                          152      152        71.0   100.4    142     81   223      2         0.9%
Northern Squaw                        337      355        24.8    82.4    320    105   425     11         5.2%
Longnose Sucker                       484      485         5.6    31.2    125    425   550     31        14.6%
Peamouth                              333      333        27.5    38.9     55    305   360      2         0.9%
Largemouth Bass                       409      409        84.0   118.8    168    325   493      2         0.9%
Smallmouth Bass                       252      284        23.5    62.2    169    140   309      7         3.3%
Pumpkinseed                           144      144        10.0    14.1     20    134   154      2         0.9%


Table 12. Flathead River, October 1998 electrofishing summary
Species/Lengths                      Mean    Median       SE     SD      Range   Min Max     Count     Percentage
Bull Trout                            484      484        34.5    48.8     69    449   518     2          0.2%
Westslope Cutthroat                   310      301        20.4    45.6    105    265   370     5          0.4%
Rainbow-Cut Hybrid                    405      414        19.9    52.5    138    349   487     7          0.6%
Rainbow Trout                         358      378        17.6    82.7    237    228   465    22          1.7%
Brown Trout                           372      381        11.5    96.3    351    210   561    70          5.5%
Mountain Whitefish                    284      300         2.1    68.7    460     0    460   1059        83.8%
Northern Pike                         587      605        14.8   129.3    558    279   837    76          6.0%
Perch                                 192      186        17.4    55.2    172    113   285    10          0.8%
Largemouth                            173      163        13.0    34.5     97    142   239     7          0.6%
Smallmouth                            252      220        34.4    76.8    184    175   359     5          0.4%


        The results of electrofishing surveys on tributaries to the lower Flathead River are
summarized in Table 13 and Table 14. The Jocko River and its tributaries have the most
significant native trout populations on the reservation. Genetic samples taken above the
Jocko Upper ―S‖ canal diversion have confirmed that the irrigation structure functions as a
fish barrier keeping the Middle and South forks of the Jocko River free of rainbow trout.
Thus, the area remains a stronghold for pure-strain westslope cutthroat trout. In all, a total
of nine separate pure-strain westslope cutthroat trout populations persist above fish barriers
in the watershed. Bull trout have been documented in the North, Middle, and South forks
of the Jocko as well as the mainstem. Introduced trout species are also well distributed
within the river. Brook trout occur throughout the drainage, but are less prevalent in the
lower reaches. Below Arlee, rainbow trout and brown trout dominate the river. Studies in


Flathead Subbasin Summary                            17                                             3/6/01
the 1980s documented an exchange of both westslope cutthroat and bull trout between the
Jocko and the Flathead rivers (DosSantos et al. 1988).
        The Jocko River is the only designated ―core area‖ and has the most significant
potential for recovery (MBTSG 1996). Core areas provide significant spawning and rearing
areas and are considered important in the overall recovery of the species within Montana
(CSKT 2000a). However, the Jocko population is currently classified as "functioning at
unacceptable risk" (Evarts, CSKT, pers. com. 2000) due to habitat degradation.

Table 13. Jocko River 1998 electrofishing summary
Species/Lengths                      Mean    Median        SE   SD      Range   Min Max     Count     Percentage
Jocko River, Dixon Reach, October 1998 Electrofishing
Brown Trout                           264      254          6    82.7    419    101   520    164        44.7%
Rainbow Trout                         287      302          9   113.8    408     74   482    168        45.8%
Rainbow-Cut Hybrid                    337      331         13    71.2    260    207   467     30         8.2%
Westslope Cutthroat                   294      309         23    51.7    113    234   347      5         1.4%
Jocko River, N. Valley Reach, September 1998 Electrofishing
Brown Trout                           222      198          6    99.0    422     88   510    260        59.5%
Rainbow Trout                         198      195         12   111.1    367     69   436     84        19.2%
Rainbow-Cut Hybrid                    317      304         31    74.8    163    242   405     84        19.2%
Bull Trout                            149      149          0     na       0    149   149      1         0.2%
Eastern Brook Trout                   248      248         19    26.2     37    229   266      6         1.4%
Mountain Whitefish                    275      282          4    82.6    350     95   445      2         0.5%
Jocko River, Spring Creek Reach, Sept. 1998 Electrofishing
Brown Trout                           242      212         12   122.0    427     89   516    105        43.8%
Rainbow Trout                         246      266         24   135.1    486     74   560     33        13.8%
Rainbow-Cut Hybrid                    436      436         33    46.7     66    403   469      2         0.8%
Eastern Brook Trout                   150      150          0     na       0    150   150      1         0.4%
Mountain Whitefish                    261      278          9    91.8    343     96   439     99        41.3%



Table 14. Crow Creek 1998 electrofishing summary
Species/Lengths                      Mean    Median        SE   SD      Range   Min Max     Count      Percentage
Reach 2 November 1998
Brown Trout                           172      143         6    72.9     327    105   432    127        22.3%
Rainbow Trout                         134     116.5        7    64.5     335     71   406     78        13.7%
Rainbow-Cut Hybrid                    152      125         4    72.7     322     85   407    263        46.2%
Largemouth Bass                       135      135         7    35.8     107     85   192     24         4.2%
Mountain Whitefish                    155      152         3    17.5     109    133   242     47         8.3%
Yellow Perch                          145      140         3    19.0      95    115   210     30         5.3%
Reach 3 November 1998
Brown Trout                           163      147          4   57.5     309    105   414    186        34.4%
Rainbow Trout                         169      150          4   66.3     486     99   585    312        57.7%
Rainbow-Cut Hybrid                    347      348         12   49.1     152    273   425     17         3.1%
Largemouth Bass                       152      153          3   12.8      47    129   176     19         3.5%
Mountain Whitefish                    168      175          5   12.2      30    150   180      7         1.3%




Flathead Subbasin Summary                             18                                           3/6/01
               Wildlife
The Flathead River Subbasin encompasses a wide diversity of habitats from its source to its
mouth. These habitats, in turn, provide niches for a diverse array of birds, mammals,
amphibians, and reptiles. Approximately 308 species of birds, 69 species of mammals,
eight species of amphibians, nine species of reptiles, and 23 species of fish occur in the
watershed (Ratti 1990; CSKT 2000).

               Target Species
               Mammals
Table 15 lists the abundance and status of target mammal species in the subbasin.

Table 15. Flathead Subbasin target mammal species
Species          Abundance      Description of Status
Elk              Abundant       Elk populations in the South, Middle and North Fork drainages experienced
                                long-term declines over the last 40 years; however, populations have
                                remained relatively stable over the last 10 years (Vore and Schmidt 1997).
                                Populations in the remainder of the basin have also been relatively stable
                                over the last 10 years.
Mule deer        Abundant       Mule deer populations throughout the subbasin have been declining over the
                                last 15 years.
Moose            Uncommon       Moose populations increased from the mid-1980’s through 1995 and have
                                subsequently experienced sharp declines.
Black bear       Common         Populations have remained relatively stable, although they fluctuate
                                depending on natural food production.
Grizzly bear     Rare           Populations are increasing in undeveloped Canadian portions of the
                                Flathead subbasin (Hovey and McLelland 1996). However, they are
                                declining to stable in the Swan Mountain Range, which is heavily impacted
                                by surrounding human developments and activities (Mace and Waller
                                1998).
Lynx             Uncommon       Lynx have historically existed at very low-densities. Current populations are
                                relatively high compared to long-term averages, in response to high
                                snowshoe hare populations.
Fisher           Uncommon       Fisher populations were supplemented with transplants during the 1950’s
                                and 1960’s. They continue to persist in the subbasin at low-densities, as they
                                have historically.
Wolverine        Uncommon       Wolverine populations exist at very low densities in the higher elevations of
                                the sub-basin. Populations have probably increased since poison baits were
                                banned in the early 1970’s.
River Otter      Uncommon



               Birds
Montana Partners-In-Flight (PIF) Bird Conservation Plan (Casey 2000) classified breeding
bird species in Montana based on their priority for conservation action within the state.
Table 16 lists the highest priority breeding bird species that are found in the Flathead River
subbasin along with their habitats and abundance. All neotropical migrant birds are also
considered target species, as are wood ducks, common goldeneye, and sandhill cranes.




Flathead Subbasin Summary                             19                                              3/6/01
Table 16. Bird species in the subbasin considered a high priority for conservation
  Species                                      Priority          Habitat                             Abundance
  Common Loon                                      I             wetland                             uncommon
  Horned Grebe                                    II             wetland                             uncommon
  Trumpeter Swan                                   I             wetland                                 rare
  Harlequin Duck                                   I             riparian                            uncommon
  Barrow’s Goldeneye                              II             wetland; riparian                   uncommon
  Hooded Merganser                                II             wetland; riparian                     common
  Bald Eagle                                      II             wetland; riparian                     common
  Northern Goshawk                                II             forest                              uncommon
  Peregrine Falcon                                II             wetland; riparian; unique               rare
  Ruffed Grouse                                   II             riparian                              common
  Columbian Sharp-tailed Grouse                   II             grassland; riparian                  extirpated
  Long-billed Curlew                               I             grassland                           uncommon
  Flammulated Owl                                  I             forest                                  rare
  Black Swift                                     II             riparian; unique                        rare
  Vaux’s Swift                                    II             riparian; forest                      common
  Calliope Hummingbird                            II             riparian; forest; shrubland          abundant
  Lewis’s Woodpecker                              II             riparian; forest                        rare
  Red-naped Sapsucker                             II             riparian; forest                     abundant
  Williamson’s Sapsucker                          II             forest                              uncommon
  Three-toed Woodpecker                           II             forest                                common
  Black-backed Woodpecker                          I             forest                              uncommon
  Pileated Woodpecker                             II             forest                                common
  Olive-sided Flycatcher                          II             forest                                common
  Willow Flycatcher                               II             riparian                              common
  Hammond’s Flycatcher                            II             riparian; forest                     abundant
  Cordilleran Flycatcher                          II             riparian                            uncommon
  Brown Creeper                                    I             forest                              uncommon
  Winter Wren                                     II             forest                                common
  Veery                                           II             riparian                            uncommon
  Red-eyed Vireo                                  II             riparian                              common
  Lazuli Bunting                                  II             riparian; shrubland                   common
  Brewer’s Sparrow                                II             shrubland                               rare
  Grasshopper Sparrow                             II             grassland                               rare
Priority Levels from Montana Bird Conservation Plan: Level I species exhibit declining populations and require
conservation plans; Level II species are under fewer threats; may be declining or stable but still must be monitored.



               Amphibians and Reptiles
Amphibians are present in many of the wetter parts of the subbasin, especially wetland and
riparian habitats. A 1993 survey of the Flathead Reservation found the long-toed
salamander, chorus frog, spotted frog, and boreal toad occur throughout the lower Flathead
drainage area, although populations of the boreal toad and spotted frog appear diminished
(Werner et al. 1995). The tailed frog occurs but is significantly more restricted in its
distribution. The leopard frog, historically common in some areas, was not found during
the survey. The survey also found that two species of garter snakes (the common and
western terrestrial) and painted turtle are common in valley and foothill habitats. The
prairie rattlesnake, bull snake, racer, and rubber boa also occur. Western skinks are thought
to be present as well, and northern alligator lizards have been documented at lower
elevations in the Mission Mountains (Tribal Wildlife Management Program Unpubl. Data).




Flathead Subbasin Summary                                   20                                                   3/6/01
Target amphibian species include the northern leopard frog, the spotted frog, and the boreal
toad.

           Threatened, Endangered, and Sensitive Species
Four federally listed wildlife species occur in the subbasin. The northern gray wolf is listed
as endangered the grizzly bear and Canadian lynx as threatened. The peregrine falcon was
recently removed from the ESA list due to recovery, and the bald eagle is proposed for
removal, but is currently listed as threatened.

           Grizzly Bear
Grizzly bears are found mainly in Glacier National Park and adjacent areas, and in and
around the Scapegoat, Bob Marshall, Great Bear, and Mission Mountains Wilderness areas
and the South Fork of the Jocko Primitive Area. The Flathead Subbasin is located within
the Northern Continental Divide Ecosystem, which is thought to contain one of the most
productive populations in the lower United States. The Canadian and U.S. portions of the
North Fork of the Flathead River Drainage support the highest density of inland grizzlies in
North America. Grizzly bear management is primarily focused on reducing human/bear
conflicts, minimizing bear mortality, and providing secure high quality habitat for bears.
Human/bear conflicts are currently the leading cause of bear mortality.

           Northern Gray Wolf
Wolves occupy several areas of the upper subbasin including parts of Glacier National Park
and the North Fork of the Flathead Valley, the Bob Marshall Wilderness, and an area to the
east of Kalispell. Wolves have also been documented on the Flathead Indian Reservation.
They occasionally pass through the reservation, and they have denned near the southern,
northern, and western boundaries. They may eventually repopulate some areas of the
reservation.
        Wolves are habitat generalists and are dependent on healthy prey populations. Big
game habitat that wolves utilize include calving and fawning areas, winter range, and
summer range. Maintaining healthy prey populations by protecting these important habitats
will help to ensure the long-term survival of the wolf within the subbasin. More direct
management, such as the protection of denning and rendezvous sites, will also be needed.

           Canada Lynx
The Canadian lynx is listed as a threatened species. The status of the lynx in the subbasin is
unknown at this time, although it is known lynx habitat exists and persistent populations
exist. Winter track surveys and remote-sensing camera surveys have detected the presence
of lynx on the Flathead Indian Reservation in potentially low densities (Tribal Wildlife
Management Program unpubl. data). Track surveys throughout the remainder of the
subbasin are detecting an increasing distribution of lynx. Studies of their status in the upper
Swan drainage and the Middle Fork of the Flathead River are underway.

           Bald Eagle
North of the Flathead Indian Reservation, bald eagle occupy habitats on the three forks and
mainstem of the Flathead River, on some of the sloughs adjacent to the river, on the north


Flathead Subbasin Summary                      21                                     3/6/01
shore of Flathead Lake, and numerous rivers and lakes throughout the remainder of the
subbasin. Twenty bald eagle breeding territories occur within the Flathead Indian
Reservation. Most of these are along the lower Flathead River, on islands or the shoreline
of Flathead Lake, or along tributaries and irrigation reservoirs. Migrant and overwintering
bald eagles may number as high as 70 birds during peak periods. Bald eagles are also
present along Flathead Lake. There are 28 occupied territories in the remainder of the
Flathead subbasin. The northern portion of the subbasin (except for Glacier National Park)
supports a productive bald eagle population. Most nests fledge one, and often two, young
per nest. One new territory has been established in each of the last two years.

               Peregrine Falcon
This species was undoubtedly once more common, but habitat destruction and the
widespread use of DDT and other pesticides have dramatically reduced the numbers. Since
banning DDT in the U.S., and with a captive breeding program in place, peregrine falcons
have increased steadily in many parts of their former range. North of the Flathead Indian
Reservation, most peregrine observations have been of migratory birds. Recently, some
residents have been observed in isolated locations such as Lower Stillwater Lake.
However, no surveys have been completed. On the Flathead Indian Reservation, the
species probably inhabited portions of the Mission Mountains and possibly the lower
Flathead River. Prior to the early 1990s, peregrines were observed as occasional migrants
during fall and spring, and were seen during the summer as recently as 1990. In the early
1990s two reintroduction sites were established on the reservation. Reintroduction has been
successful at both of these sites, and two additional nesting territories may be productive
during 2001.

               Sensitive Species
The tribes and state classify 39 terrestrial, vertebrate wildlife species in the subbasin as
sensitive (Table 17). All are considered sensitive due to low populations, threats to their
habitats, or highly restricted distributions. These species do not necessarily have legal
protection but are considered sensitive to human activities and attention to their habitat and
population needs may be warranted during the planning of resource management activities.
The status of many of these species is not known because there have been few population
or habitat studies.

Table 17. Sensitive species
 Amphibians
 Boreal toad                       Tailed frog
 Birds
 Common loon                       Common tern
 American white pelican            Forster’s tern
 Black-crowned night-heron         Black tern
 White-faced ibis                  Yellow-billed cuckoo
 Trumpeter swan                    Flammulated owl
 Harlequin duck                    Burrowing owl
 Bald eagle                        Great gray owl
 Northern goshawk                  Boreal owl
 Ferruginous hawk                  Black swift



Flathead Subbasin Summary                           22                                3/6/01
 Peregrine falcon                  Black-backed woodpecker
 Columbian sharp-tailed grouse     Loggerhead shrike
 Black-necked stilt                Baird’s sparrow
 Franklin’s gull                   Le conte’s sparrow
 Caspian tern
 Mammals
 Townsend’s big-eared bat          Woodland caribou
 Northern bog lemming              Wolverine
 Gray wolf                         Fisher
 Grizzly bear                      River Otter
 Lynx


             Habitat Areas and Quality
Although fish and wildlife are separated in the discussion that follows, the quality of
habitat in riparian and wetland areas as well as upland areas affect both fish and wildlife.
Upland areas that have been heavily roaded or overgrazed affect big game populations, but
they also can contribute sediment to waterways impacting fish and other aquatic organisms.
Similarly, when wetlands and riparian areas are lost or degraded, both fish and terrestrial
wildlife species suffer. Conversely, habitat improvements in upland areas that are designed
to benefit wildlife usually have beneficial effects on fish, just as measures designed to
rehabilitate riparian and wetland areas for fish almost certainly benefit wildlife.

             Fish
Barriers to trout movement in the upper part of the subbasin are shown in Plate 11 of
Appendix B. Plates 12 through 16 show the general quality of habitat for westslope
cutthroat trout and bull trout in the upper part of the subbasin.

             North, Middle, and South Forks of the Flathead River
In the headwaters of the Flathead Subbasin, fish habitat quality is high. Headwater reaches
are largely undeveloped in Glacier National Park, the Bob Marshall and Great Bear
Wilderness, Jewel Basin, and other national forest lands. They retain a high percentage of
the original wild attributes and native species complexes. Protection of these remaining
pristine areas and reconnection of fragmented habitats in the subbasin are high priorities.
        The remainder of the upper subbasin ranges from extremely degraded to nearly
pristine. Many stream reaches have been blocked to fish passage by man made or natural
barriers. Outside of the South Fork of the Flathead drainage, approximately one-third of the
spawning areas in the upper half of the subbasin have been degraded by excessive sediment
inputs, which have decreased egg-to-fry survival to <30 percent (Weaver and Fraley 1991;
1993). An additional one-third of the remaining spawning reaches are inhabited by
introduced fish species that can compete or hybridize with genetically "pure" native stocks.

             Hungry Horse Dam Impacts on Fish Habitat
Hungry Horse Dam impounds the 4,403-km2 South Fork drainage basin. Completion of
Hungry Horse Dam in 1952 on the South Fork of the Flathead River inundated 124 km of
high-quality spawning and rearing streams. Fish passage structures were never installed in
the dam, which became operational in 1953.


Flathead Subbasin Summary                             23                            3/6/01
        Complete replacement of this inundated stream habitat is not possible. However,
mitigation efforts are underway to protect, re-open, or reconstruct the remaining tributary
habitat to offset the loss.
        Reservoir drawdowns have ranged as deep as 188 feet, exposing over 70 percent of
the reservoir area to desiccation and erosion. Drawdown affects all biological trophic levels
and influences the probability of subsequent refill during spring runoff. Refill failures are
especially harmful to biological production during the productive warm months. Annual
drawdowns impede revegetation of the reservoir varial zone, resulting in a littoral zone of
nondescript cobble/mud/sand bottom with limited habitat structure.
        Power operations cause rapid fluctuations in dam discharges (as great as 400
percent change in daily discharge), which are inconsistent with the normative river concept.
Flow fluctuations widen the riverine varial zone, which becomes biologically
unproductive. Implementing watershed-based dam operations to recover all native species
(Marotz et al. 1999) can mitigate this effect.
        Hungry Horse Dam operation reversed the Flathead River hydrograph for power
and flood control and altered the annual temperature regime, causing impacts typical of
dam tailwaters. As part of Hungry Horse mitigation, a selective withdrawal, temperature
control structure was installed on Hungry Horse Dam. The device restored naturalized
water temperatures to 71 river kilometers of the mainstem Flathead River. Model estimates
predict a two to three-fold increase in growth potential for the fish that remain in the
affected reach due to temperature control. Sampling is ongoing to document the influence
on target species and their prey.
        Fish passage problems in tributaries to Hungry Horse Reservoir were documented
following the reconstruction of roads to accommodate higher water levels (Morton 1955;
MT Fish and Game Commission 1963). Sixteen percent of the existing westslope cutthroat
trout and bull trout spawning and rearing habitat above full-pool elevation was blocked by
poorly placed culverts (MDFW&P and CSKT 1991). Natural barriers include beaver dams
and sections of stream channels that intermittently become dry due to subsurface water
flow.
        An unforeseen benefit of Hungry Horse Dam is that it has prevented introduced fish
species in the lower Flathead system from accessing Hungry Horse Reservoir and its
tributaries.

           Kerr Dam Impacts on Fish Habitat
The Kerr Dam project is located on the lower Flathead River approximately 7.2 km
downstream from the natural outlet of Flathead Lake. The project includes a 200 foot-high,
381 foot-long dam, a 126,000-acre reservoir, three penstocks, and a powerhouse containing
three generating units, each rated at 60 megawatts. Annual operations of the Kerr Project
affect the first 35-km of the upper Flathead River, the entire Flathead Lake shoreline, and
the entire 116 km of the lower Flathead River below Kerr Dam.
        Seasonal lake-level fluctuations associated with Kerr Dam operations are
considered responsible for causing adverse impacts to shoreline and near-shoreline
fisheries habitats. Under the current Federal Energy Regulatory Commission (FERC)
license, continued manipulation of the Flathead Lake hydrograph will result in shoreline
habitats (those located within the varial zone, which lies between lake-level elevations


Flathead Subbasin Summary                     24                                     3/6/01
2,893 feet and 2,883 feet) being inundated from June through late fall of every year. Lake
levels are then gradually reduced to low pool level (2,883 feet) by April 15, after which the
lake-filling cycle begins again. This artificial hydrograph differs from Flathead Lake’s
natural hydrograph. Under natural conditions, the lake typically filled to approximately
2,893 feet during the annual June snowmelt period. It then dropped fairly rapidly until it
reached approximately 2,883 feet in late summer. The adverse habitat effects of these
continued operations include: (1) winter dewatering of preferred shoreline spawning areas
for salmonids; (2) degradation of deep spawning habitat (below elevation 2,883 feet) by
distribution of fine sediments (a consequence of shoreline erosion during the extended full-
pool period); (3) and degradation of varial zone and deeper spawning and rearing habitats
for non-salmonid fishes and invertebrates resulting from a reduction in the time of
beneficial wave cleaning action due to extended deep-water periods over these habitats.
These direct habitat impacts, which limit shoreline invertebrate and juvenile fish
production, result in indirect negative impacts to the foraging habitats of other fish species,
including native bull and cutthroat trout (FERC 1996, MPC 1990).

           Flathead Indian Reservation (Lower Flathead River Drainage)
           General Description
The fisheries resources of the Flathead Indian Reservation have been affected by a variety
of human activities. The initial and probably greatest influence has been the construction
and operation of the Flathead Indian Irrigation Project. Historic impacts from irrigation
include stream dewatering, the blockage of migration routes by diversion structures, and
the loss of large numbers of fish as water is diverted into the canal system. Another major
influence on the reservation fisheries has been the introduction of exotic species. These
introductions have produced some thriving fisheries, but have reduced native populations
through competition and hybridization. Agriculture and grazing have influenced fisheries
by degrading water quality and modifying stream bank vegetation. The primary influence
from past forestry practices has been extensive road construction in watersheds, which has
resulted in increases in sediment and encroachment on channels. The current goal for
reservation forests is to achieve a total road density of less than 6.5 miles of road per
square mile by removing 15 percent of road spurs in currently roaded areas.
        Between 1994 and 1997 the tribes collected samples from 15 streambeds using the
McNeil coring method (McNeil and Ahnell 1964). The samples were from sites in both the
commercial and noncommercial forest. For each stream the samples contained an average
content of particles less than 4.75 mm in diameter ranging from nine to 40 percent.
        Between 1993 and 1997 the University of Montana Riparian and Wetland Research
Program evaluated 102 reaches of stream on the reservation. The average score for all
reaches was 74, which is described as a functional riparian condition, but considered at risk
if remedial management actions are not taken. Of the 102 inventoried reaches, 15 rated as
nonfunctional, 46 were functional-but-at-risk, and 41 were in proper functioning condition.

           Lower Flathead River
The lower Flathead River is unique in its geology and temperature regime. The river cuts
through highly erosive lacustrine and alluvial sediments deposited during the life span of
glacial Lake Missoula. Cottonwood habitat types and a mixed deciduous/coniferous


Flathead Subbasin Summary                        25                                    3/6/01
overstory has been forced toward a conifer-dominated overstory due to the abatement of
periodic flooding activity and constrained flows under recent peaking operations
(DosSantos et al. 1988). Kerr dam operations historically had significant impacts to the
riparian community due to load-following and power-peaking practices. Many of these
impacts were addressed in 1997 when the facility was changed to a "baseload" operation
under the new license agreement. Current monitoring under mitigation programs centers
around assessing the benefits to the biotic community. The river channel itself is largely
unaltered by development. The railroad cut off several meander bends or side channels
between the town of Dixon and its confluence with the Clark Fork River, but the channel is
considered relatively stable. Current impacts to fish habitat quality include bank trampling
and vegetation disturbances from grazing and elevated fine sediment input and
temperatures from its major tributaries and irrigation return flows. However, due to its size
relative to these impacts, fish habitat quality in the mainstem river remains largely
unaltered from historic conditions.
        Naturally high water temperatures occur in the river, primarily due to the
configuration of Flathead Lake. A large shallow bay near the outlet of the lake results in
high water temperatures that decrease habitat quality for native salmonids in the lower
Flathead River, at least seasonally (Hansen, CSKT, pers. com. 2000). During the summer,
lower Flathead River water temperatures are 3 to 4° C higher than those recorded in the
upper Flathead River above Flathead Lake due to the natural warming of the lake. Summer
water temperatures in the main river are near 20° C, as much as 10° C warmer than any
lower river tributary inflow. Winter temperatures reach 0.0° C. The average annual water
temperature is 9° C (DosSantos et al. 1988).

           Tributaries
The overall health of fish habitat in the upper Jocko River is good to fair. In the lower
reaches where water courses have been channelized, water quality degraded, and flows
altered, it is poor (CSKT 2000a). Adding to these impacts are problematic irrigation
diversions. Important trout spawning areas have been degraded by sedimentation
(DosSantos et al. 1988); the sediment originating from irrigation returns and poor riparian
management.
         The habitat quality of all the tributaries to the lower Flathead has suffered
significant adverse impacts due to the construction and operation of the Flathead Indian
Irrigation Project and general agricultural practices. In general, impacts include the
trapping of fish in unscreened irrigation diversions, frequent, erratic changes in streamflow
below irrigation diversions, return flows laden with silt, reduced gravel recruitment in
streams, and blocking of access to spawning and rearing habitat.

           Cutthroat Trout and Bull Trout Habitat on the Reservation
Populations of cutthroat and bull trout on the Flathead Reservation have been greatly
reduced from pre-European levels, and because many of today's populations are not secure,
the decline is continuing. Reasons for the decline include impacts from irrigation practices,
the introduction of exotic species, and habitat degradation. Artificial migration barriers
have isolated many populations. The barriers have hastened the demise of some
populations but protected others by preventing exotic species from invading. Habitat


Flathead Subbasin Summary                          26                                3/6/01
condition will likely stabilize or improve if road densities decrease and road standards
improve.
         Six populations of bull trout survive within the Flathead Indian Reservation. Prior
to the construction of dams, adults from these populations may all have shared habitats
within the Flathead River and Flathead Lake. Today, three populations are isolated behind
dams at the base of the Mission Mountains. They spawn in streams within noncommercial
forest lands and are most vulnerable to changes in dam operations and to hybridization
with non-native brook trout. There is no timber harvest or roading planned within the
ranges of these three populations. The population of bull trout that resides in Flathead Lake
spawns off the reservation and is only minimally influenced by forestry activities on the
reservation. The populations that reside in the Jocko and Flathead rivers are the most
subject to influence by forestry activities. Much of its range is in the forks of the Jocko
River, in areas that are noncommercial forest lands. The Jocko population is currently
classified as "functioning at unacceptable risk" (Evarts, CSKT, pers. com. 2000). Primary
causes for this ranking are identified as habitat fragmentation from irrigation diversions
within the Jocko drainage and mainstem Clark Fork River dams. Other impacts include
irrigation dewatering, riparian degradation, channelization, and competition from exotic
species.
         By 1999, the Tribal Fisheries Program had identified 21 separate populations of
pure-strain westslope cutthroat trout. Most of these are isolated behind barriers and are
widely distributed across the forested landscape. Perpetuation of these populations will
require protecting habitat, reducing fragmentation, and separating them from introduced
brook and rainbow trout.

           Subbasin-wide Bull Trout Habitat Risk Factors
The Montana Bull Trout Study Group identified and rated various habitat risk factors in the
subbasin. The major habitat risk factors for the species include: (1) rural residential
development especially around Flathead Lake, the North and South forks of the Flathead,
and the Swan River; (2) dam operations in the areas affected by Kerr and Hungry Horse
Dam operations; (3) forestry practices throughout the subbasin; and (4) agriculture and
grazing in the lower Flathead River drainage. These activities have lowered habitat quality
for bull trout and threaten to continue to do so in the future.

           Wildlife
           Priority Habitats
Wildlife habitats that are considered management priorities within Flathead River Subbasin
include the following:

           Riparian Deciduous Forest (Cottonwood/Aspen), Mixed Forest (Deciduous/Conifer), and Riparian
           Shrublands
The habitat integrity and availability of riparian deciduous forest and riparian shrublands
have been compromised in many parts of the subbasin, and there are continued threats to
these habitats. Generally, degradation has resulted either through interruption or alteration
of natural flood processes, or through direct removal of vegetation through grazing,



Flathead Subbasin Summary                         27                                            3/6/01
clearing, or logging. Changes in flow regimes can have a profound effect on the mix of
seral stages present along river reaches, as cottonwoods require flooding and silt deposition
for germination. In many cases where the seasonal pattern of high flows has been removed
or stabilized, there is a threat of inadequate recruitment to replace older trees as they die. In
the most extreme examples of flow alteration—dewatering on the one hand and inundation
through damming on the other—all riparian habitat values can be lost.
        Mixed forest riparian habitat exhibits co-dominants of cottonwood and ponderosa
pine. These are habitat types in successional transition, generally with the coniferous type
in some stage of achieving dominance over the cottonwood type. These types provide a
large number of niches for a wide variety of wildlife species, but it is likely that in the
future they will offer less diverse habitat due to succession toward a dominant conifer type.
        Specific activities, which have the most direct effects on riparian habitats, include:

       •   Flood control and channelization through rip-rapping and other means;
       •   Dam construction and operation;
       •   Logging, particularly of older cottonwoods for lumber or pulp;
       •   Water diversion for irrigation;
       •   Clearing for agriculture (crops, hay, pasture);
       •   Grazing;
       •   Residential development; and
       •   Recreational use.

           Riparian Coniferous Forest
Many upper elevation reaches are in good to excellent condition because of their
inaccessibility. Fire suppression has altered species composition in some areas by favoring
western red cedar, western hemlock, and grand fir over seral species such as western larch,
sub-alpine fir, and lodgepole pine. Lower and mid-elevation reaches are more susceptible
to the pressures of overgrazing, flood and erosion control efforts, irrigation withdrawals,
road building, logging, and firewood cutting. Long-term grazing impacts in low elevation
stands have reduced shrub, forb, and grass cover and created open understory conditions.
Grazing has also destabilized stream banks and increased erosion.

           Prairie Wetlands
Prairie wetland habitats occur in the Mission Valley, and significant conversion of these
habitats has occurred there. Pothole habitats have also been impacted by the loss of
surrounding uplands from conversion to croplands, degradation of uplands due to
overgrazing, subdivision, contaminated runoff from agriculture, selenium contamination
(from leaching due to irrigation or saline seeps), invasion by exotic plants (purple
loosestrife), road building and filling. Wildlife values of many wetlands have also been
dramatically reduced due to fragmentation, isolation, and high disturbance levels from
subdivision and resultant high homesite densities.

           Intermountain Valley Wetlands
Unquantified but substantial wetland losses in the subbasin have resulted mostly from
filling or draining for subdivisions and agriculture. Intermountain wetlands have also been


Flathead Subbasin Summary                      28                                       3/6/01
impacted by development of surrounding uplands (especially cabins and rural subdivisions
along shorelines), contaminants, invasion of non-native plants (purple loosestrife),
introduction of non-native fish, and disturbance from increasing recreational use.

           Intermountain Grasslands
The most immediate threat comes from conversion of existing native grasslands to other
types. Conversion primarily occurs in three ways—urban sprawl, establishing tame
pastures, and conversion to cropland. Another major concern is the introduction and spread
of noxious weeds, particularly knapweed. Other management issues include: 1) grazing
regimes, 2) replacement of fire regimes, 3) fragmentation of existing grasslands, and 4)
shrub and tree encroachment.

           Dry Forest (Ponderosa Pine/Douglas-fir)
The major change common to most dry forest types (especially ponderosa pine) in Montana
and elsewhere in the American West is a profound alteration in age-class structure,
physical structure, tree density, and tree species composition as a result of logging and fire
suppression. Stands that were largely dominated by mature and old growth ponderosa pine
trees in an open-parkland setting have been changed to abnormally dense stands dominated
by younger Douglas-fir trees.

           Moist Douglas-Fir/Grand Fir
The combination of logging and fire suppression has produced a more homogeneous
landscape dominated by mid-seral forests, as opposed to historical conditions where more
young and old growth forest existed.

           Whitebark Pine
Whitebark pine is associated with the federally listed grizzly bear, which relies on
whitebark pine nuts. An assessment of the interior Columbia River Basin found that the
amount of area in whitebark pine cover type has declined by 45 percent since the turn of
the century. This decline, which has been due to a combination of factors (the most
prominent of which are mountain pine beetle and whitepine blister rust), has had strong
negative consequences for grizzly bears. Most of the loss occurred in the more productive,
seral whitebark pine types, of which 98 percent has been lost.

           Aspen
Aspen trees are in poor condition in many areas of the subbasin. Most of the aspen
remaining are in the older age classes and are in critical need of regeneration. Older stands
are usually less vigorous and the least likely to regenerate successfully. Competing conifers
are currently crowding out many of these stands. Aspen will eventually be lost from these
sites. In addition, pure and mixed stands in the older age classes are of low vigor and are
often heavily infested with pathogens. Effective fire suppression over the past 50 years has
permitted competition and disease to reduce clone vigor to levels lower than would be
expected under natural conditions. Compounding the situation, fire suppression has
drastically reduced fire-induced regeneration resulting in few younger-aged stands. Many



Flathead Subbasin Summary                            29                              3/6/01
stands have also been converted to pasturelands or can be classed as a grazing disclimax
with little or no regeneration because of heavy grazing pressure.

           Upper Flathead Subbasin habitat areas of special concern
Key areas within the Flathead Subbasin critical to native species restoration are
experiencing a rapidly progressing change in land ownership and management patterns.
Subdivision and residential development of agricultural and timberlands adjacent to
waterways in the drainage poses one of the greatest threats to sensitive riparian wildlife.
Plum Creek Timber Company, a major landholder in the Flathead drainage, is currently
divesting itself of large tracts of its lakeshore and streamside holdings basin-wide. Growth
of small tract development throughout the area and its tributaries is occurring at a record
rate.

           Flathead Indian Reservation (Lower Flathead River Drainage) habitat areas of special concern
Plate 17 in Appendix B shows habitat areas of special concern for wildlife on the Flathead
Indian Reservation. This map is not inclusive, however. Wetlands, stream corridors, and
riparian areas are important for wildlife but could not be effectively mapped at this scale. In
addition, there are many other unmapped dispersed or local sites on forested and open
lands that are valuable wildlife habitat. Zone 1 habitat for grizzly bears constitutes critical
habitat and recovery areas. Zone 2 habitat is the area immediately adjacent, is occupied by
grizzly bears, and that has the potential to be reclassified to Zone 1.
        In many parts of the Flathead Indian Reservation human activities continue to
diminish wildlife habitats. Perhaps the most noticeable changes are reductions in the ranges
of larger carnivores such as the northern gray wolf and grizzly bear. Another significant
change is loss of big game winter range due to high road densities, housing developments,
and competition with livestock. In addition, the habitats of other species have been altered
by fire suppression, logging, grazing, various forms of development, and the introduction
of exotic plant and animal species. Fire suppression alone has had major consequences. For
example, at low elevations, open stands of old ponderosa pine, which provided important
habitat for many wildlife species, have been converted to dense thickets of Douglas-fir. At
higher elevations, fire exclusion policies have meant fewer natural openings, which also
provide important habitat. Although there is still great ecological diversity on the Flathead
Reservation, humans have altered many of the natural ecological processes that influence
wildlife habitats. Arresting the degradation and managing wildlife for the long-term benefit
of tribal members is one of the tribes’ highest priorities.

           Flathead Lake
The wildlife habitat along the edge of Flathead Lake has changed greatly since the
beginning of operations at Kerr Dam due to changes in the natural hydrograph coupled
with seasonal flooding of an additional ten vertical feet of lake shoreline habitats. The
desiccation and flooding regime existing under past and current operations of Kerr Dam
have adversely impacted 1,792 acres of wetland and riparian habitat along the shoreline of
the lake. These habitat changes will not be repaired under the current and future operations.
Under past operations, shallow bays, which were emergent marshes during much of the
year, became either dry mudflats or inundated shallow areas, depending upon the time of


Flathead Subbasin Summary                        30                                            3/6/01
year. Other areas that supported riparian vegetation were affected by higher and longer
water levels and were converted to areas of bare ground due to inundation (Mackey et al.
1987, Mack et al. 1990). The altered hydrograph has created a more stable annual
hydrograph, which has allowed for homesite development on most of the lake shoreline,
with an attendant level of wildlife habitat loss or degradation.
           Lower Flathead River
The annual hydrograph for the lower Flathead River shows a reduction in peak flows and
an increase in winter flows from the pre-impoundment hydrograph. These changes in flows
cause the normally vegetated varial zone to become abnormally inundated. Similar to the
lake, this does not allow riparian vegetation to exist where it normally would. This is
especially true in the lower half of the river’s course. The area between the high and low
water levels of these two reaches has become a largely unvegetated zone dominated by
mud and rock. Deciduous and mixed deciduous/coniferous vegetation has moved toward a
conifer-dominated vegetative community due to the curtailment of periodic flooding
activity and constrained flows under recent peaking operations. Studies have also shown
that constant fluctuation in water levels and flows have not allowed a stable enough
situation for vegetation to become established (Mackey et al. 1987, Mack et al. 1990,
Hansen and Suchomel 1990). Other habitat impacts associated with Kerr Dam include:
dewatering of the floodplain, which has resulted in the direct loss of approximately 6,731
acres of riparian area and accelerated the conversion of riparian areas to agricultural lands
and livestock grazing; a reduction in the recruitment of early successional riparian species
such as cottonwood and sandbar willow; and wetland losses (2,352 acres) within the zone
of fluctuating water levels (CSKT 2000b).

           Other Habitats
The Mission Valley contains a (unique), high density of prairie pothole wetlands. Tributary
streams trend from low sinuosity, gravel-bedded streams near the mountain front, to more
sinuous or winding silt and gravel-bedded streams near the valley floor. Several small
valley-floor tributaries or segments of tributaries (in addition to Ronan Spring Creek) are
sustained by ground-water discharge. Many reservation streams contain excellent wetland
and wet meadow habitats. Adjacent uplands are largely used for agriculture, primarily
pasture and hay and grain production. The lower part of many of the drainages encompass
scattered shrub-dominated and grassland sites bordered mainly by irrigated agricultural
lands used for pasture and hay production.

           Watershed Assessment
Watershed assessments are an important tool for identifying projects and limiting factors.
Past studies and habitat surveys provide extensive assessment-type data.
        In 1977, the U.S. Congress funded an "overview environmental impact study" to
assess the impacts of population growth and proposed natural resource development in the
Flathead River Subbasin. The study, which ran from 1978 to 1985, was funded through the
Environmental Protection Agency and included a significant program of basic research on
the condition of the subbasin's water, land, air, and socio-cultural resources. The most
intensive research effort was directed toward aquatic systems on Flathead Lake and its
major tributaries. In all, more than one hundred original research documents were produced


Flathead Subbasin Summary                    31                                      3/6/01
during the course of the study. Among the most significant assessments were fish and
habitat inventories of streams in the North and Middle Forks drainages of the Flathead
River (Read et al. 1982 and Weaver et al. 1983).
         In the 1980s and 1990s, Bonneville Power Administration (BPA) funded a series of
fish and wildlife studies in the basin as part of the agency's program to protect, mitigate,
and enhance fish and wildlife affected by the development and operation of hydroelectric
facilities on the Columbia River and its tributaries. Under this funding, MDFW&P
conducted studies of kokanee in Flathead Lake (Decker-Hess and Clancey 1984) and the
upper Flathead River (Fraley 1984). The agency also examined Hungry Horse-caused
fishery losses in the Flathead system (Zubik and Fraley 1987) and studied Canada geese
(Casey et al. 1984) in the northern Flathead Valley. The Confederated Salish and Kootenai
Tribes studied Canada geese in the southern Flathead valley (Mackey et al. 1985) and the
fishery in the lower Flathead system (DosSantos, et al. 1988).
         The Forest Plan for the Flathead National Forest, completed in the mid-1980s
contains assessment information for those portions of the subbasin managed by the US
Forest Service (Brannon, E.B. 1985).
         Under contract with the U.S. Bureau of Indian Affairs (BIA), staff of the Flathead
Lake Biological Station studied the aquatic insects of the lower Flathead River (Hauer and
Potter 1986). Among the other assessment-type reports authored in part or whole by
Flathead Lake Biological Station personnel are: Baseline water quality conditions for the
North Fork Flathead River, British Columbia and Montana (Appleman et al. 1990);
Hydrologic data for the North Fork Flathead River, British Columbia and Montana
(Appleman et al. 1990); Limnology of Flathead Lake; and Water Quality Data and
Analyses to Aid in the Development of Revised Water Quality Targets for Flathead Lake,
Montana (Stanford et al. 1997). The station has also issued numerous water quality
monitoring reports for the lake and tributaries and conducted many aquatic surveys and
research investigations in the subbasin. It maintains an extensive scientific database on a
variety of fisheries-related aspects of lake limnology and other related topics.
         In 1987, MDFW&P issued a report titled Effects of Water Level Fluctuations on
Aquatic Furbearer Distribution, Abundance and Habitat in the Northern Flathead Valley
(Bissell and Brown 1987). The project was designed to determine the effects of Kerr Dam
on semi-aquatic furbearers in the upper Flathead. Another effort focused on the effects of
water level fluctuations on ospreys and bald eagles in the upper Flathead. Both these
projects were coordinated with similar efforts conducted for the BIA in the lower Flathead
drainage (Mack et al. 1990).
         The Montana Riparian and Wetland Association conducted a riparian inventory of
the lower Flathead River in 1990. The association also gathered riparian condition data on
selected reservation watersheds from 1993 to 1997 (MRWA, unpublished data 1993-97).
         The MDFW&P and CSKT issued the Hungry Horse Dam Fisheries Mitigation
(1991) and Implementation Plan (1993) for losses attributed to the construction and
operation of Hungry Horse Dam. In 1985, MDFW&P issued the Wildlife and Wildlife
Habitat Mitigation Plan for Construction of Hungry Horse Dam (Bissell and Yde 1985).
The mitigation plans quantify fish and wildlife losses and mitigation actions above and
below Hungry Horse Dam, as called for by the Northwest Power Planning Council’s
(NWPPC) Columbia Basin Fish and Wildlife Program (Program).


Flathead Subbasin Summary                   32                                      3/6/01
        In 1992 the CSKT completed a management plan for the lower Flathead River that
compiled general assessment information, especially on human use (CSKT 1992). National
Wetlands Inventory maps were produced for the Flathead Indian Reservation in 1992 under
a cost-share agreement between the tribes and USFWS. In 1995 the CSKT issued a report
on the status of amphibian and reptiles on the Flathead Indian Reservation (Werner et al.
1995).
        The BIA completed an Environmental Impact Statement (EIS) for the segment of
the Yellowstone Pipeline that cuts through the southern part of the Flathead Indian
Reservation. The document contains assessment information for watersheds along the
pipeline route, most notably, the lower Flathead River west of Dixon.
        Bull trout assessments and recovery actions are coordinated with the Montana Bull
Trout Scientific Team, USFWS, and BC Environment. In the mid-1990s, the Montana Bull
Trout Study Group compiled a series of bull trout status reports. Status reports that include
waters within the Flathead Subbasin are (1) Middle Clark Fork River including the lower
Flathead River to Kerr Dam; (2) Flathead Lake, including the North and Middle forks of
the Flathead River and Stillwater and Whitefish Rivers (3) South Fork of the Flathead
River, upstream of Hungry Horse Dam; and (4) Swan Lake/River. These status reports are
intended to provide the most current and accurate information available to the Bull Trout
Restoration Team and local bull trout watershed groups.
        In 1996, Makepeace and Mladenich documented the contribution of nearshore
nutrient loads to Flathead Lake.
        In 1997 the Flathead Basin Commission issued a report prepared by the Flathead
Lake Biological Station titled Water Quality Data and Analyses to Aid in the Development
of Revised Water Quality Targets for Flathead Lake, Montana. The report examines long-
term trends and relationships in Flathead Lake nutrient loading data and in-lake responses
from the long-term monitoring program. It also presents the results of synoptic studies
done during 1995-6 that was designed to better understand anthropogenic sources of
nutrients from within the watershed.
        Research and monitoring of the threatened bull trout and the petitioned westslope
cutthroat trout is a collaborative effort between MDFW&P and CSKT. The backbone of
the existing fisheries knowledge on Flathead Lake comes from data collected over many
years by the fisheries co-managers—CSKT and MDFW&P. North of the lake, most of the
work is conducted by MDFW&P, south of the lake, by CSKT. Deleray and others (1999)
summarize recent survey work done by MDFW&P and CSKT. The work summarized in
this report includes: (1) Flathead Lake monitoring (annual relative fish abundance surveys,
lake trout otolith analysis, lake trout tagging, lake trout food habits study, Mercury and
PCBs in fishes, angler creel surveys, kokanee reintroduction test, bioenergentic modeling;
(2) Hungry Horse Reservoir gill net surveys; (3) Flathead River mainstem and South,
Middle and North Fork monitoring (water temperature monitoring and assessment of
selective withdrawal, westslope cutthroat trout abundance estimates, Flathead River winter
trout abundance, and angler cutthroat trout tagging project); and (4) tributary stream
monitoring (streambed coring, substrate scoring, stream electrofishing/juvenile salmonid
abundance estimates, and bull trout redd counts).
        Fisheries assessment data collected by and held at the MDFW&P Kalispell office
includes: annual counts of spawning redds in index streams correlated with periodic basin-


Flathead Subbasin Summary                    33                                      3/6/01
wide redd surveys; site specific redd counts and migrant trapping to document the strength
of spawning runs before and after habitat restoration and /or fish passage improvements;
mark/recapture and extinction method population estimates and annual or seasonal gill net
surveys to document population trends and community structure; angler creel census
(watershed-wide and site specific); photo-point documentation of habitat improvements;
quantitative habitat surveys; sediment coring and scoring in spawning areas, correlated
with results of fry emergence trapping over the range of sediment types; measures of fish
growth, fecundity and condition factor that can be related to environmental factors; water
temperature monitoring specifically related to riparian restoration and the selective
withdrawal structure on Hungry Horse Dam; and measures of total available habitat and
habitat use as related to dam discharge.
        In 1998, CSKT and MDFW&P prepared the Dayton Creek Watershed Restoration
Progress Report Information pertaining to limiting factors, water quality, fish species
present, and riparian function are contained in this report (DuCharme et al. 1998).
        CSKT (Makepeace 1998) described stream channel morphology at reference
reaches in forested watersheds on the Flathead Reservation.
        The Wetlands Conservation Plan for the Flathead Indian Reservation (Price 1999)
contains general assessment-type information for wetland and riparian areas on the
reservation.
        In 2000, the CSKT issued a comprehensive report titled: Nonpoint Source
Assessment for Stream, Rivers, Lakes, and Wetlands of the Flathead Indian Reservation. It
describes watershed analysis areas, places waterbodies within attainability groups, and
outlines existing tribal programs and resource management efforts that can address
nonpoint source management issues (Makepeace 2000).
        The CSKT completed a forest management plan and EIS in 2000 for over half a
million acres of forest land on the Flathead Indian Reservation. Both the EIS and the draft
and final plan contain general assessment information on forested reservation watersheds
within the reservation (Rockwell et al. 2000).
        A watershed plan for the Jocko River Watershed on the Flathead Indian
Reservation was completed in 2000. This document compiles all existing natural resource
information for the Jocko River (CSKT 2000).
        The Fish and Wildlife Implementation Strategy and Annual Reports for the Kerr
Mitigation Project (CSKT 2000b) contain assessment information for watersheds on the
Flathead Reservation.
        Other water quality assessment information comes from work currently in progress
by the Flathead Basin Commission (FBC), University of Montana Yellow Bay Biological
Station, and the Confederated Salish and Kootenai Tribes. This includes water quality
monitoring done by the FBC as well as work done in conjunction with MDFW&P through
FBC’s Volunteer Monitor Program. Yellow Bay Biological Station conducts water quality
analyses in their mid-Flathead Lake studies. The Confederated Salish and Kootenai Tribes
have a Water Quality Program which tracks water quality within the reservation’s
boundaries. This program also monitors water supply or streamflow discharge monitoring,
fluvial geomorphology, sediment levels, and the presence/absence of aquatic invertebrates
to determine lake, stream, and river health.




Flathead Subbasin Summary                   34                                      3/6/01
        A great deal of the data that has been collected in various assessments conducted
within the subbasin have been digitized and are stored in various Geographic Information
System (GIS) databases. The CSKT Natural Resources Department and the Montana State
Library (the Montana Natural Resource Information System (NRIS) and the Montana
Rivers Information System MRIS keep the databases).

             Limiting Factors
At almost six million acres, the Flathead Subbasin is roughly the size of New Hampshire.
Because habitats and land uses vary across such a large area, the limiting factors in the
subbasin also differ, depending on where you are. The following list groups the subbasin
into six zones based upon the major types of waterbodies and land uses and lists the
primary limiting factors for each. The list is followed by a brief description of each of the
limiting factors.


Headwaters and Associated Uplands (includes all mountain tributaries)
     Fragmentation
     Sedimentation (fish)
     Non-native Species Interactions (fish and wildlife)
     Vegetation Change (fish and wildlife)

Impoundments (includes Hungry Horse Res., Flathead Lk, Swan Lk, and irrig. impoundments)
     Non-native Species Interactions (fish)
     Fragmentation of Habitat (fish and wildlife)
     Cultural Eutrophication — Flathead Lake only (fish)
     Inundation and Water Fluctuations (fish and wildlife)

Regulated Mainstems (includes South Fork, Upper Flathead, Lower Flathead, Jocko River)
     Altered Hydrograph (fish and wildlife)
     Floodplain Alterations – includes bank instability and floodplain restrictions (fish and wildlife)
     Non-native Species Interactions (fish)

Unregulated Mainstems (includes North Fork, Middle Fork, and Swan Rivers)
     Non-native Species Interactions (fish and wildlife)
     Fragmentation of Habitat (wildlife)
     Human/Wildlife Conflicts (fish and wildlife)

Valley Tributaries & Wetlands (includes all valley tributaries and the Whitefish and Stillwater Rivers)
     Floodplain Alterations (fish and wildlife)
     Sedimentation (fish)
     Non-native Species Interactions (fish and wildlife)
     Temperature Changes (fish)
     Fragmentation of Habitat (fish and wildlife)
     Human/Wildlife Conflicts (fish and wildlife)

Lakes (includes connected and closed-basin lakes)
     Non-native Species Interactions (fish and wildlife)
     Human/Wildlife Conflicts (fish and wildlife)
     Alteration of the Littoral Zone (fish and wildlife)
     Cultural Eutrophication (fish)


Flathead Subbasin Summary                             35                                             3/6/01
           Alteration of the Littoral Zone
The Flathead Subbasin has experienced significant growth and development over the past
twenty years, much of it near or adjacent to lakes and streams. The result has been the loss
of significant riparian and wetland areas, which is some of the most important fish and
wildlife habitat in the subbasin. These areas are important because so many species depend
on them. For example, of the 256 resident and migratory bird species that occur on the
Flathead Indian Reservation, 142 depend on wetlands and riparian areas for one or more of
their habitat requirements. These areas are used by many of the subbasin's threatened,
endangered, and sensitive species, for example: trumpeter swans, bald eagles, grizzly bears,
boreal toads, and leopard frogs.
        Wetlands and riparian areas also provide much of the food consumed by a number
of fish species. In addition, they serve as nurseries and spawning areas. The loss of riparian
areas has resulted in a net loss of security cover, bank stability, and pool formation.

           Altered Hydrograph
Hydropower related discharge fluctuations on the South Fork and upper mainstem of the
Flathead River have resulted in a wider zone of water fluctuation, or varial zone, which has
become biologically unproductive. Reduction in natural spring freshets due to flood control
has reduced the hydraulic energy needed to maintain the river channel and periodically re-
sort river gravels. Collapsing riverbanks caused by intermittent flow fluctuation and lack of
flushing flows have resulted in sediment buildup in the river cobbles, which is detrimental
to insect production, fish food availability, and security cover. Changes in the annual
hydrograph for the lower Flathead River cause the normally vegetated varial zone to
become abnormally inundated. This does not allow riparian vegetation to exist where it
normally would. The area between the high and low water levels has become a largely
unvegetated varial zone dominated by mud and rock. Deciduous and mixed
deciduous/coniferous vegetation has moved toward a conifer-dominated vegetative
community due to the curtailment of periodic flooding activity and constrained flows under
recent peaking operations. Studies have also shown that constant fluctuation in water levels
and flows have not allowed a stable enough situation for vegetation to become established
(Mackey et al. 1987, Mack et al. 1990, Hansen and Suchomel 1990).

           Cultural Eutrophication
Open-water primary production is a main measure of water quality in lakes like the
Flathead. This is a very sensitive measure of the ability of a lake to grow algae. Lakes
polluted with plant-growth nutrients, particularly nitrogen and phosphorus, typically have
high rates of primary production, poor water clarity due to blooms of algae, and bad tastes
and odors associated with the decomposition of the blooms. These are symptoms of a
process called eutrophication, which in its worst stages can result in floating mats of blue
green algae and dense growths of aquatic macrophytes. Over the long-term, primary
production has steadily increased in Flathead Lake, although the rate of increase slowed
substantially in the mid-1990s. The reduction has been due primarily to substantial
improvements in the Flathead Basin's urban sewage treatment plants during the period


Flathead Subbasin Summary                    36                                      3/6/01
from 1989 to 1993, which reduced human sources of nutrient pollution by about 15 percent
(Stanford 1999). However, in 1997 and 1998, nitrogen concentrations in the Stillwater
River and the upper mainstem Flathead River were among the highest levels ever
recorded. Anthropogenic sources of nitrogen and phosphorus in those rivers include runoff
from hard surfaces (parking lots, city streets) and near-shore housing construction, poorly
managed farm and timberlands and groundwater pollution from faulty household drain
fields. The long-term record shows that as much as 40 percent of the annual input of
phosphorus to Flathead Lake comes from the airshed. The nutrient is contained in
particulates from slash and other burning and fugitive dust from rural roads. This so-called
"nonpoint nutrient loading" in the Flathead Basin is a very serious pollution problem and it
is getting worse.

           Floodplain Alterations
Channelization, road fill, bank armoring and other encroachments along stream segments
have narrowed channels and limited meander inside floodplains. This has created shorter
channels, steeper gradients, higher velocities, loss of storage and recharge capacity, bed
armoring, and entrenchment. In impacted stream reaches, even minor flood events have
often resulted in significant deterioration. Erosion has increased, and the number of pools
and the extent of riparian cover has decreased. The changes have lowered the quality of
fish and wildlife habitat.

           Fragmentation of Habitat
Fish migrations have been blocked from other man-caused barriers, including road
culverts, dewatered stream reaches, irrigation diversions, etc. For wildlife, fragmentation
has been caused by a combination of human and natural factors. Human factors include
timber harvesting, housing development, power transmission lines, hydroelectric
development, and road construction. Fragmentation has had negative effects on many
species, but it has especially affected species like lynx, fisher, and pileated woodpecker that
require large, contiguous forest patches. Species like elk, mule deer, and sharp-tailed
grouse, that need large open patches, have also suffered from human-caused fragmentation.

           Human/Wildlife Conflicts
Increasing numbers of humans in sensitive wildlife habitats has led to an increasing
number of human/wildlife conflicts. For example, increasing residential development and
recreational activities has resulted in an increase in human-caused grizzly bear mortality. It
has led to winter recreationists displacing wintering elk; jet skis disturbing nesting loons,
and poachers illegally harvesting bull trout. Humans continue to introduce non-native fish
species that impact native species restoration efforts.

           Inundation and Water Fluctuations
When Hungry Horse Reservoir filled, 124 km of high quality stream habitat was lost.
Filling of the reservoir also inundated large areas of low elevation forest, wetland, and
riparian habitats, including seasonal habitat for a wide variety of avifauna, spring and fall
grizzly bear habitat, and important big game range and calving areas. Excessive reservoir


Flathead Subbasin Summary                     37                                       3/6/01
drawdowns now expose vast expanses of reservoir bottom to drying, thus killing aquatic
insects, which are the primary spring food supply. Reduced reservoir pool volume impacts
all aquatic trophic levels due to the diminished size of the aquatic environment. During
summer, reservoir drawdown reduces the availability of terrestrial insects for fish prey
because fewer insects are trapped on the diminished surface area. Impoundment by Hungry
Horse Dam and the removal of riparian vegetation altered the annual temperature cycle in
the river. These changes have affected the food base for the many wildlife species that feed
on aquatic organisms.
        Seasonal lake level fluctuations associated with Kerr Dam operations are
considered responsible for causing adverse impacts to shoreline, near-shoreline fisheries
habitats, and the Flathead River upstream of the lake. Under the current FERC license,
continued manipulation of the Flathead Lake hydrograph will result in shoreline habitats
being inundated from June through late fall of every year. The adverse habitat effects of
these continued operations include: (1) winter dewatering of preferred shoreline spawning
areas for salmonids; (2) degradation of deep spawning habitat (below elevation 2,883) by
distribution of fine sediments (a consequence of shoreline erosion during the extended full-
pool period); (3) and degradation of varial zone and deeper spawning and rearing habitats
for non-salmonid fishes and invertebrates resulting from a reduction in the time of
beneficial wave cleaning action due to extended deep-water periods over these habitats.
These direct habitat impacts, which limit shoreline invertebrate and juvenile fish
production, result in indirect negative impacts to the foraging habitats of other fish species,
including native bull and cutthroat trout (FERC 1996, MPC 1990). Shallow bays, which
were emergent marshes during much of the year, are now either dry mudflats or inundated
shallow areas, depending upon the time of year. This has eliminated habitat for wildlife.
Other areas that supported riparian vegetation, including 35 km of the Flathead River
upstream of Flathead Lake, have been affected by higher water levels for longer periods;
have been converted to areas of bare ground due to inundation and subsequent dewatering
(Mackey et al. 1987, Mack et al. 1990). These changes have affected the food base for the
many wildlife species that feed on aquatic organisms.

           Non-native Species Interactions
Non-native species now threaten the diversity and abundance of native species and the
ecological stability of ecosystems in the subbasin. Illegal and unintentional introductions of
non-native fish species have set up negative inter-species competition with native fish.
Non-native species have also hybridized with native species. Conversely, impoundment
has greatly benefited the native northern pikeminnow and peamouth chub, which now
compete with or prey upon species of special concern for food and space. The introduction
of opossum shrimp (Mysis relicta) into the Flathead system has had serious repercussions
on the Flathead Lake kokanee salmon. The introduction of kokanee salmon and lake trout
into Flathead Lake may have adverse effects on native bull and westslope cutthroat trout.
Bullfrogs on the lower Flathead River have displaced native chorus and spotted frogs. The
quality of fish and wildlife habitat has been reduced or eliminated by a host of exotic plants
(noxious weeds) able to out-compete native species.




Flathead Subbasin Summary                     38                                       3/6/01
            Sedimentation
Logging activities, road building, residential development, and agricultural practices have
increased the amount of fine sediments entering streams. Fine sediments accumulating in
spawning substrates reduce egg-to-fry survival. In some areas sedimentation has reduced
natural reproduction to the point that it is insufficient to fully seed available rearing habitat
with juvenile fish. Pools and rearing habitat have become clogged with sediment, reducing
the productive capacity of the stream. Sediment has also killed aquatic insects and algae.
All of these changes have affected the food base for the many wildlife species that feed on
aquatic organisms.

            Temperature Changes
The removal of riparian vegetation, especially trees and overhanging shrubs, has changed
stream water temperatures, making the water warmer in the summer and colder in the
winter. These changes have interfered with fish spawning and generally degraded the
quality of stream habitats for native fish and other aquatic life. This has affected the food
base for the many wildlife species that feed on aquatic organisms.

            Vegetation Changes
Fire exclusion policies and logging have fundamentally transformed the structure and
composition of subbasin forests. At lower elevations, dense thickets of Douglas fir have
replaced open park-like stands of ponderosa pine. Mid-elevation forests, which historically
formed a complex mosaic composed of many different patch sizes, age structures, and
species, have become much more uniform. As a result, there has been a significant loss of
habitat diversity, and habitats important to some species, like the grizzly bear, have become
much less common. The changes have also altered runoff patterns, which has adversely
affected fish and other aquatic organisms.

            Artificial Production
A Hatchery Genetics Management Plan (HGMP) for the Creston National Fish Hatchery is
included in Appendix A. The bull trout facility at the Creston Hatchery allows for
experimental culture of bull trout in captivity. Initially, gametes from wild adults were
hatched to provide eggs, fry, and fingerlings for an imprint-timing experiment. Developing
eggs, fry, and fingerlings were incrementally sacrificed to measure thyroxine hormone
levels, a surrogate for determining when the fish imprint on their water source. Remaining
juveniles were reared through adult stage and spawned in captivity. Progeny have provided
a source for experiments on temperature sensitivity and susceptibility to whirling disease.
This benefited the listed population through increased knowledge and by reducing the need
to take individuals from wild stocks.
        Approximately 50,000 rainbow trout and 60,000 cutthroat trout are reared at
Creston annually to provide subsistence and recreational fisheries for tribal and non-tribal
anglers in closed-basin lakes on the Flathead Indian Reservation. Approximately 20,000
westslope cutthroat trout were propagated at Creston in 1999 and 35,000 in 2000 for
release in closed-basin lakes in State-managed waters. Nearly all of the offsite lakes
planted under this program do not support natural reproduction. Where natural


Flathead Subbasin Summary                      39                                        3/6/01
reproduction is possible, the primary objective is to create genetic reserves for isolated
populations of native stocks. In these cases, habitat restoration is performed to enhance fish
passage and natural reproduction in the closed system. This hatchery program does not
supply fish to waters scheduled for native species restoration. The closed-basin lakes that
are planted through this program provide alternative fisheries to meet public demands for
harvest and partially offset fishing bans or reduced limits enacted for native species
recovery. This program may indirectly benefit native species recovery by redirecting
harvest away from sensitive recovery areas in the contiguous Flathead watershed.
Rehabilitated lakes remove undesirable species that are a source for additional illegal
introductions (e.g. illegally introduced yellow perch, northern pike, sunfish, fathead
minnow and in one case, grass carp). Occasionally, illegal introductions occur after lakes
have been reclaimed and fisheries established. This negatively impacts the program. An
additional chemical treatment may be required within approximately ten years. During the
interim, fisheries established by this program remain viable until the undesirable
introduced fish become reestablished.
        The offsite lakes program is monitored through periodic gill net surveys, angler
interviews, and the annual statewide angler creel survey. Stocking rates are established to a
large degree by trial and error. Gill netting provides data on species relative to abundance,
growth rates, and fish-condition factor. Angler surveys are qualitative indicators of catch
rates, angler satisfaction, and rough estimates of harvest. Although rigorous quantitative
analyses of CPUE, survival, and total harvest are possible, the number of lakes involved
makes this level of monitoring economically impractical. Rigorous sampling is reserved for
aspects of the Hungry Horse Mitigation Program directed toward native species restoration.
        Qualitative assessments have shown that small, closed-basin lakes yield an efficient
hatchery-plant to angler-creel ratio. Project lakes are put, grow, and take fisheries, entirely
dependent on artificial production to support the fishery. Many have been chemically
rehabilitated to remove illegally introduced species. Gill netting, site visits to interview
anglers, and an annual statewide angler creel survey provide managers with qualitative
information on species composition, growth, condition factor, and angling success.
Periodic spot checks at individual lakes have revealed great success. For instance, angler
pressure on Lion Lake grew to the highest small lake in Region One.

           Sekokini Springs Natural Rearing Facility and Interpretive Center
Sekokini Springs was a private trout pond that propagated rainbow trout for purchase by
private pond owners. Unfortunately the site probably leaked rainbow trout into the Flathead
River, where they were a threat to the native westslope cutthroat population. Evidence
suggests that rainbow trout escaped for nearly 40 years. The Hungry Horse Mitigation
program first leased the site to remove all rainbow trout from the facility. After removing
trout from the water source and performing a comprehensive analysis for fish diseases, the
State fish health specialist listed the Sekokini Springs water source as safe for experimental
culture of westslope cutthroat trout. The program then bought the improvements on the US
Forest Service property and secured a no-cost special use permit for use of the site by
MDFW&P and CSKT.
        With the cooperation of the USFWS Creston National Fish Hatchery,
approximately 40,000 fingerling westslope cutthroat (designated pure strain M012 brood


Flathead Subbasin Summary                     40                                      3/6/01
source) were reared to assess the water source at Sekokini Springs. The water source
follows a natural annual flow and temperature regime that successfully raised westslope
cutthroat with an exceptional condition factor. The M012 fish were planted in closed-basin
lakes. There are no fish at the site at this time.
         Sekokini Springs is in step one of the NWPPC's three-step Artificial Review
Process. A genetic management plan is being developed prior to any additional fish being
moved to the site. Three spring sources that provide water to the small hatchery building
and outdoor rearing streams will be capped to protect the site from fish diseases.
Partnerships have been formed with the U.S. Bureau of Reclamation (BOR) and U.S.
Forest Service to develop a master plan for the site. Other groups (such as Trout Unlimited
and Boy Scouts of America) have shown interest in cooperating on renovating the habitat
at the site. BOR has contributed $70,000 for an interpretive pathway featuring water
conservation. Future plans for the pathway include two fish viewing areas and exhibits
explaining the need for native species restoration. Future plans are to allow for natural
reproduction of westslope cutthroat from the Flathead River and experimental outdoor
rearing of up to six genetic strains of wild cutthroat trout from the Flathead watershed. The
genetic management plan and future uses are being drafted for peer review. Needs for local
genetic strains include restoration of wild runs where natives have been extirpated to
replace hybridized populations in headwater lakes that are threatening pure westslope
cutthroat trout stocks downstream in each drainage.
         Periodic spot checks at individual lakes stocked with M012 cutthroat trout from
Sekokini Springs have revealed great success. For instance, Rogers Lake now supports a
genetic reserve for Red Rocks Lake fluvial grayling (provided by the state of Montana
hatchery system) and a major fishery for westslope cutthroat trout (Knotek et al. 1997).

           Existing and Past Efforts
           Summary of Past Efforts
From 1982 through 1985, MDFW&P and CSKT compiled biological data needed to
construct the quantitative reservoir model HRMOD. With aid from Montana State
University (MSU), the U.S. Geological Survey (USGS), BOR, Army Corps of Engineers
(ACOE) and scientific reviews, Montana completed the model and developed Biological
Rule Curves (BRCs) for Hungry Horse Dam (first published in 1989). The BRCs were
integrated with power and flood control during the Columbia Basin System Operation
Review, and by 1995 the Integrated Rule Curves were completed and adopted by the
Northwest Power Planning Council (NWPPC). The IRCs were subsequently superseded by
operations dictated by the National Marine Fisheries Service (NMFS) and have not been
fully implemented to date.
        Habitat restoration efforts outlined in the Mitigation Plan have been completed or
are ongoing. Monitoring and evaluation of restoration techniques and fish population
responses continues. Cooperative programs and projects have been established with a
variety of other entities for ongoing agency management and regulatory activities.
        MDFW&P modeled the potential of retrofitting Hungry Horse Dam with a
temperature control structure to modify downstream temperatures. This selective
withdrawal structure was funded through a congressional appropriation and became



Flathead Subbasin Summary                    41                                      3/6/01
functional in 1996. Temperatures have been returned to naturalized conditions in 71 km of
the mainstem Flathead River.
        Kokanee reintroduction was attempted but unsuccessful in Flathead Lake from
1992 through 1997. That program at the USFWS Creston National Fish Hatchery has now
shifted to using standard and experimental hatchery techniques to hatch and rear native
species at low densities for restoration stocking and to create fishing opportunities in
closed-basin lakes using native, and where appropriate, non-native trout. Public education
and new angling opportunities are being used to redirect angling pressure and harvest away
from sensitive recovery areas.
        In the first 24 months, the CSKT Focus Watershed Program began coordinating and
assisting in several local projects including Dayton Creek, the east and south forks of
Valley Creek, Marsh Creek, Post Creek, Mission Creek, DuCharme Creek, the Little
Bitterroot River, and Jocko River. The watershed coordinator has worked closely with the
Flathead Basin Commission, Bull Trout Restoration Team, Lake, Lincoln, Sanders, and
Flathead County Conservation Districts, NRCS personnel, tribal personnel, Montana
Watercourse, Montana Watershed Inc., and several locally led community interest groups.
       Over 10,000 acres of wildlife habitat have been enhanced or conserved through
mitigation projects funded in partnership with BPA since the 1970s. This work has resulted
in over 4,000 acres of mitigation credit for wildlife habitat losses associated with Hungry
Horse Dam. MDFW&P have completed 21 percent of upland forest losses, and 29 percent
of riparian/wetland losses. Table 18 summarizes acres of wildlife habitat lost to
hydroelectric development, mitigation accomplished through July 2000, and mitigation
remaining for each component of the program.

Table 18. Acres of wildlife habitat lost to hydroelectric development, mitigation
accomplished through July 2000, and mitigation remaining
                            Hungry     Hydropower       Mitigated     Mitigation
Habitat Category             Horse       Losses       through 7/00    Remaining
Riparian/Wetland              6,876      5,226           1,500         3,726
Upland Forest                16,804     12,771           2,701        10,070
Total                        23,680     17,997           4,201        13,796

        Kastler (1998) completed a graduate study of elk reproductive success in the South
Fork of the Flathead River. In 1996, Bissell completed the Hungry Horse and Libby
Riparian/Wetland Habitat Conservation Implementation Plan, which describes the means
by which MDFW&P will implement this program from 1996 through 2006 (Bissell 1996).
Mace and Waller (1997) provided a compilation of published and unpublished data
obtained from radio instrumented grizzly bears in the Swan Mountains. Their report
includes information on resource selection, denning ecology, spatial and temporal
interactions, and grizzly relationships to the human environment, activity and time budgets,
and demography and population trends.




Flathead Subbasin Summary                    42                                     3/6/01
           Accomplishments by Year
           1992
MDFW&P completed a study examining the enhancement of benthic insect production in
Hungry Horse Reservoir. The study concluded that insect production can be enhanced
through installation of slash piles, but the practice was not implemented fully because its
cost effectiveness was questionable.
        MDFW&P completed a chemical rehabilitation of Lion Lake in which illegally
introduced perch and pumpkinseed were removed. The lake is located approximately 1.6
km from Hungry Horse Reservoir. The project restored the trout fishery and increased
angler use nearly ten-fold. The lake had the highest angler pressure per acre among some
500 lakes in northwestern Montana.

           1993
Brook trout were eradicated and spawning and rearing habitat was enhanced in Elliott
Creek, a direct tributary to the Flathead River. The project partially met the biological
objective in that brook trout eradication was not complete, but cutthroat trout were
established. They spawned and offspring were reared in improved habitat.
        MDFW&P completed the offsite chemical rehabilitation of Rogers Lake in which
perch were removed and cutthroat trout and arctic grayling were reestablished. The lake is
now a genetic reserve for the rare Red Rocks Lake strain of arctic grayling.

           1994
CSKT completed the 1992-93 Flathead Lake Creel survey.
        MDFW&P chemically rehabilitated Devine Lake, successfully eradicating non-
native brook trout in order to reduce the hybridization threat to bull trout in Hungry Horse
Reservoir, one of the strongest remaining populations.
        MDFW&P also completed a bank stabilization and sediment abatement project at a
massive landslide in Big Creek, a major bull trout-spawning stream. The slide was directly
above a known spawning area. The large bank slump was re-vegetated and stabilized,
reducing sediment inputs to bull trout spawning areas downstream.

           1995
CSKT reconstructed groundwater seepage on Polson Golf Course into a stream channel
flowing into Flathead Lake.
        MDFW&P completed sediment-source surveys on road systems associated with six
major, connected, bull trout spawning tributaries to Hungry Horse Reservoir.
        MDFW&P completed a cooperative culvert-improvement project on Margaret
Creek, a direct tributary to Hungry Horse Reservoir. The project opened 3.8 km of high
quality habitat. Adfluvial cutthroat redds and juvenile bull trout are now upstream of a
former culvert barrier.
        MDFW&P also completed thermal modeling and the installation of selective
withdrawal structures on Hungry Horse Dam to restore normative river temperatures
(Marotz et al. 1994; Christenson et al. 1996). Thermal targets are now being met (1996-




Flathead Subbasin Summary                    43                                     3/6/01
98). The response of benthic invertebrates and fluvial fish is being evaluated in the
Flathead River.

           1996
         A fish ladder at Taylor's Outflow was completed to allow access for spawning
populations of cutthroat trout in the Flathead River. A trap weir now excludes rainbow
trout attempting to enter the stream. Westslope cutthroat trout used the ladder in 1997-98
and gained access to restored spawning and rearing habitat.
MDFW&P completed baseline data collection of bull trout spawning habitat quality and
utilization in reservoir and backcountry tributaries of the South Fork Flathead River to
monitor population trends and spawning and rearing habitat quality.
         MDFW&P completed cooperative fish-passage projects replacing culverts on
Murray and Riverside Creeks, tributaries to Hungry Horse Reservoir. The project opened 7
km of quality habitat. Adfluvial cutthroat trout redds and juvenile bull trout are now above
the culvert barrier.
         MDFW&P completed a fish passage and habitat enhancement project at Hay Creek,
a tributary to the North Fork Flathead River. The lower reaches of this stream no longer
flow subsurface, a condition that created a passage barrier, during the summer and support
native trout.
         MDFW&P completed willow-survival experiments in the drawdown zone of
Hungry Horse Reservoir and examined methods for re-establishing vegetation in the varial
zone. The project identified survival rates for different willow species and the duration of
inundation in a drawdown zone.
         In 1996 MDFW&P completed an offsite chemical rehabilitation of Bootjack Lake
in which introduced pumpkinseed were removed and westslope cutthroat and rainbow trout
were introduced. The trout fishery is now recovering. The lake has fish up to 20 inches in
length and is fished heavily.
         MDFW&P also completed the development of Integrated Rule Curves (IRCs) for
Hungry Horse Reservoir (Marotz et al. 1996; updated 1999).

           1997
MDFW&P completed cooperative culvert-improvement projects on seven Hungry Horse
Reservoir tributaries. The purpose of the project was to eliminate passage barriers for
adfluvial cutthroat trout. It resulted in 16 percent more spawning and rearing area in
Hungry Horse Reservoir.
         MDFW&P completed the offsite chemical rehabilitation of Murray and Dollar
lakes. Illegally introduced fathead minnows and redside shiners were removed and trout
were re-established. Fishing improved dramatically.
         MDFW&P completed a food habits study for lake trout and northern pikeminnow
in the Flathead River. Researchers collected and analyzed over 850 stomachs and estimated
species-specific losses to predation (Malta et al. 1997; Zollweg 1998). The project
quantified the diet composition of the primary predator in the Flathead System, which is
believed to be a major limiting factor for native trout.




Flathead Subbasin Summary                    44                                         3/6/01
           1998
MDFW&P completed a study quantifying zooplankton entrainment at Hungry Horse Dam
under various operational scenarios using selective withdrawal (Cavigli et al. 1998). The
results provided dam operators with instructions for using the duel intake ports.
        MDFW&P completed offsite chemical rehabilitation of Little McGregor Lake in
which illegally introduced perch were removed. Trout were re-established in the lake in
1999.
        MDFW&P completed the Griffin Creek fencing project, which excluded cattle
from 8 km of stream containing genetically pure westslope cutthroat trout.
        MDFW&P completed the construction of the Crossover Wetlands project in which
a subsurface diversion structure was installed to expand the wetland in the reservoir varial
zone. The wetland has expanded over several acres. Biological monitoring is ongoing.
        MDFW&P completed the development of a basin-wide radio-telemetry monitoring
system for the upper Flathead River drainage. Seasonal movement studies on lake trout and
northern pike were completed, and habitat use and movement studies on bull trout and
westslope cutthroat trout were initiated.
        MDFW&P completed the channel reconstruction of 2 km of Taylor's Outflow
spring creek, which improved habitat complexity and channel stability in the spawning
reach.
        CSKT completed a channel reconstruction in Skidoo Creek to allow passage of fish
through a culvert barrier.
        CSKT completed a channel reconstruction in Skidoo Creek to allow passage of fish
through a culvert barrier and cost-shared riparian fencing in Valley View with Pheasants
Forever to exclude stock from irrigation canal/creek entering Flathead River.
        CSKT completed monitoring of the Flathead Lake kokanee experiment.
        CSKT completed the Dayton Creek Watershed Restoration Progress Report and the
Focus Watershed Project contributed cost-share to a Small-Landowner workshop
sponsored by Montana DNRC and to the Flathead Basin Commission for a voluntary
monitoring program.
        CSKT revised a grazing plan for East Valley Creek and constructed a riparian and
headwater fence.

           1999
MDFW&P completed a fish passage improvement project on Paola Creek, a major
spawning tributary to Hungry Horse Reservoir. A culvert barrier was removed and baffles
were installed to allow fish passage.
        MDFW&P initiated a contract for stream survey and design work with Land and
Water Consulting to reconstruct the lower 1.6 km of Emery Creek, a major spawning
tributary to Hungry Horse Reservoir.
        CSKT and MDFW&P established livestock management agreements and
eliminated point sediment/nutrient sources (e.g. fencing and streambank stabilization) in
Dayton Creek.
        MDFW&P pursued land acquisition and developed preliminary channel-and-pond-
complex designs for Sekokini Springs Natural Rearing Facility. The water source proved to
promote impressive growth and condition factor of westslope cutthroat trout.


Flathead Subbasin Summary                   45                                      3/6/01
         MDFW&P began a westslope cutthroat trout hybridization risk assessment in the
mainstem of the Flathead River in addition to stepping up the commitment to remove
compromising genetic material from high-elevation lakes in the North, Middle and South
Fork drainages.
         MDFW&P completed a riparian fencing project in lower Hay Creek to exclude
cattle in conjunction with a USFS grazing allotment modification.
         MDFW&P completed project-specific monitoring and evaluation of ongoing and
completed projects throughout the Flathead River drainage (i.e. Taylor's Outflow, seven
Hungry Horse Reservoir tributaries, Crossover Wetland Area, Hay Creek, Griffin Creek,
and area lakes).
         MDFW&P completed a site evaluation, feasibility analysis, constant flow rate and
water quality tests, and landowner scoping for Rose Creek stream/pond project.
         MDFW&P monitored watershed level fish and habitat parameters in cooperation
with fish management staff and other agencies. Efforts included population surveys,
streambed coring, redd counts, and gillnetting (ongoing since 1991).
         MDFW&P initiated an Instream Flow Incremental Methodology study (IFIM) in
cooperation with Miller and Associates (Fort Collins, CO) on the Flathead River. The
study targets size-classes of native bull trout and westslope cutthroat trout.
         CSKT completed the 1998-99 Flathead Lake Creel survey.
         CSKT constructed over 7,000 feet of riparian fence and 200 feet of livestock
exclusion corral panels in cooperation with landowners and MDFW&P to exclude
livestock from the riparian area along the mainstem of Dayton Creek.
         CSKT constructed 200 feet of livestock exclusion corral panels in cooperation with
a landowner and MDFW&P to exclude livestock from the riparian area; constructed 5.6 km
of riparian fence on the Middle and East forks of Dayton Creek in cooperation with Plum
Creek; constructed 2.7 km of riparian fencing along Valley Creek; constructed 800 feet of
livestock-exclusion fence along DuCharme Creek; completed habitat restoration projects
on the Redhorn Range Unit; and wildlife habitat improvements through prescribed burning
in the Boulder and Ferry Basin areas.
         CSKT made land acquisitions along the Mission Front and constructed fences to
deter grizzly bear conflicts.

           Ongoing Fisheries Projects
A comprehensive study is being conducted in collaboration with the University of Montana
to examine the degree and threat of hybridization between native cutthroat trout and non-
native rainbow trout throughout the Flathead River drainage. Construction has begun on
the Emery Creek project. A wetted perimeter study is nearing completion in the South
Fork downstream of Hungry Horse Dam to calculate a new minimum flow requirement for
the reach. Spring caps are being installed at Sekokini Springs. Population electrofishing
surveys, bull trout redd counts, whirling disease sampling, spring migrant trapping, and
radio-telemetry surveys are being completed for the Flathead River drainage. A winter
growth analysis of westslope cutthroat trout in headwater populations will be completed
soon.




Flathead Subbasin Summary                   46                                     3/6/01
           Ongoing Wildlife Projects
MDFW&P has been conducting a 12-year study of white-tailed deer in coniferous forests
of northwestern Montana to develop techniques to determine basic biological and
ecological parameters for white-tailed deer and relate those parameters to characteristics of
individual habitats and potential limiting factors. Final reports for this project are
scheduled for 2002.
        MDFW&P have two full-time positions to deal with human/wildlife conflicts in
northwestern Montana. With this focus, the Department has developed innovative
techniques using aversive conditioning to teach grizzly bears to avoid potential conflict
situations. They are also involved in an information and education program to provide
public information on how to coexist with wildlife. These people, along with regular
wardens and biologists, respond to hundreds of calls resulting from situations where
wildlife presence is either undesirable or poses a public safety issue. The workload
continues to increase as more people move into previously undeveloped wildlife habitat.
Similar activities are undertaken by the CSKT on reservation lands where the activities are
conducted by tribal wildlife biologists and conservation officers.
        MDFW&P and CSKT are expanding their efforts to educate all hunters. These
efforts are intended to decrease game law violations and cases of mistaken identity, foster
increased public acceptance of hunters and hunting, and to improve relationships between
hunters and landowners. This is being accomplished through development of advanced
hunter education classes and other information and education efforts.
        Wildlife surveys and inventories are conducted annually on a variety of game,
furbearer, and non-game species in the subbasin by state, tribal, and federal agencies. Also,
MDFW&P conducts annual hunter harvest surveys to monitor population trends and
demographic patterns in harvested wildlife populations.
        Tribal, local, state and federal agencies annually spend significant sums of money
for the control of various noxious weeds found in the Flathead Subbasin.
        Tribal, state and federal natural resource management agencies, as well as some
large corporate landowners have been involved in interagency efforts to recover listed
species of fish and wildlife. These efforts include active management activities to protect
listed species and their habitats, reduce or mitigate adverse impacts of various human
developments, protect important habitats, reduce species mortality, and reduce direct
human/wildlife conflicts.
        From 1993 through 1997, MDFW&P purchased 475 acres of land in the Mission
Valley. These lands are the latest additions to their 3,462-acre Ninepipe Wildlife
Management Area that is managed to provide food and cover for local wildlife populations.
The area includes numerous pothole wetlands that have been created or restored.
        The CSKT has a proactive land acquisition program that aims to re-acquire the
reservation land base. Much of this land is then subjected to inter-disciplinary planning
processes, in which wildlife habitat values are considered. In addition, the CSKT is
currently acquiring wetland and riparian habitats and adjacent upland habitats under
mitigation planning processes for Kerr Dam and for off-reservation mining impacts. When
these tracts are acquired they will be managed for fish and wildlife benefits.
        Currently in the upper portion of the Flathead River Subbasin, there are two
ongoing habitat enhancement projects being conducted in cooperation with the Flathead



Flathead Subbasin Summary                    47                                      3/6/01
National Forest. Both projects are designed to enhance 6,000 acres of important wildlife
habitat adjacent to Hungry Horse Reservoir. The Firefighter Mountain Project (900 acres)
is nearing completion. The Paint/Emery Project (5,100 acres) will begin in fiscal year 2000.
In addition, the goal to conserve or enhance 5,303 acres of riparian and wetland habitats in
the Flathead River Subbasin over the next 45 years is considered an ongoing habitat
conservation project.
         On the Flathead Reservation, the CSKT have developed several habitat restoration
and enhancement projects for the benefit of riparian, aspen seep, and wetland habitats.
Many of these projects are in the initial stages of development or have recently been
completed. Several other projects will be initiated during the next few years.
         In an effort to restore viable populations of extirpated species on the Flathead
Reservation, the CSKT have successfully re-introduced the peregrine falcon and have
restored the species as a breeding bird. Current efforts aimed at the restoration of
trumpeter swans are also underway. Planning efforts are underway to restore Columbian
sharp-tailed grouse and the northern leopard frog.
         The final settlement of the Confederated Salish and Kootenai Tribes’ mitigation
claims related to the construction and operation of Kerr Dam will be completed during the
fall of 2000. This settlement includes provisions for the acquisition of 985 acres of wetland
and riparian habitat to replace varial zone habitat lost due to the operations of Kerr Dam on
the lower Flathead River. It also includes provisions for acquisition of 312 acres of riparian
habitat. For Flathead Lake impacts, the settlement dictates acquisition of 1,792 acres of
wetland habitat to replace lakeshore varial habitat that was lost.
         Habitats acquired under the settlement will be restored to provide the optimal
wildlife habitat and productivity. In addition, other opportunities for restoration at other
sites on the reservation will be pursued. Wildlife monitoring will center on representative
habitat tracts and existing and acquired habitats to gauge the degree of change in wildlife
status following restoration activities. It will also maintain long-term population
monitoring of particular species. Wildlife habitat monitoring will be conducted to
determine the success of various restoration and enhancement actions.
         The Jocko River Watershed Restoration Program is a large-scale watershed
restoration project directed at the restoration of riparian and wetland habitat and
enhancement of native bull trout populations. This program will involve acquisition and
management of wetland, riparian, and adjacent habitats and management of these tracts to
benefit fish and wildlife resources.


Present Subbasin Management

           Existing Management
Federal, state, county and tribal governments have management authority within this
subbasin. Table 19 (adapted from Zackheim 1983) shows the major administrative
authorities in the subbasin and their holdings. The U.S. government controls slightly more
than half of the land, most of that is administered by the U.S. Forest Service. The majority
of the southwestern part of the subbasin—from the middle of Flathead Lake south—falls
within the Flathead Indian Reservation and is administered by the Confederated Salish and


Flathead Subbasin Summary                    48                                      3/6/01
Kootenai Tribes of the Flathead Indian Reservation. The Canadian portion of the subbasin
includes 274,280 acres administered as British Columbia Crown Lands.

Table 19. Flathead River Subbasin land ownership
 Ownership                                                   Acres
 Private Lands
    Corporate Timber                                          274,372
    Other Private                                           1,567,022
 Confederated Salish and Kootenai Tribal Lands
    Tribal Lands (total)                                     669,064
          Mission Mountains Tribal Wilderness                 92,000
          Thompson Peak Tribal Wilderness                      4,800
          Sleeping Woman Tribal Wilderness                    17,600
          Tribal Primitive Areas                              98,000
 State Lands
    Department of State Lands
         Coal Creek State Forest                              15,064
         Stillwater State Forest                              93,815
         Swan River State Forest                              38,345
         Other State forest lands                             41,749
         Other State lands                                     1,722
    Montana Fish, Wildlife & Parks Lands                       3,025
 Federal Lands
    Glacier National Park                                    614,882
    Flathead National Forest
          Bob Marshall Wilderness Area                        709,356
          Great Bear Wilderness Area                          286,700
          Mission Mountains Wilderness Area                    73,877
          Jewel Basin Hiking Area                              15,000
          Other forest lands                                1,264,999
    US Fish and Wildlife Service
          National Bison Range                                18,540
          Pablo & Ninepipe National Wildlife Refuges           4,523
          Swan River National Wildlife Refuge                  1,576
          Other federal wildlife lands                         4,555


        In 1982, the Ninth Circuit Court of Appeals handed down a judgement that the bed
and banks of the southern half of Flathead Lake are held by the U.S. in trust for the Salish
and Kootenai Tribes. This decision gives the CSKT the authority to regulate the fishery in
the southern half of the lake and protect fishing rights given to them by the Hellgate Treaty
of 1855 (Vashro, et al. 1989).
        The U.S. portion of the subbasin, all of which lies in Montana, includes all of Lake
County, most of Flathead County, some of Sanders County, and small portions of
Missoula, Lincoln, Powell, and Lewis and Clark counties. The major towns are Whitefish,
Columbia Falls, and Kalispell in the north and Polson, Ronan, Hot Springs, St. Ignatius,
and Arlee in the south. No significant settlements occur in the Canadian part of the
subbasin.
        The following is a list of the major entities having regulatory/management authority
in the subbasin and a short description of their responsibility areas.




Flathead Subbasin Summary                              49                            3/6/01
           Federal Government
           U.S. Forest Service
The U.S. Forest Service (USFS) manages approximately 40 percent (2,349,932 acres) of
the subbasin. USFS policies and federal legislation guide management of these lands.
Management guidelines are contained in the Flathead National Forest Land and Resource
Management Plans and in more site-specific planning and environmental documents.

           Bonneville Power Administration
The Bonneville Power Administration (BPA) operates the federal Columbia River
hydropower system as if it were a single owner enterprise to maximize power efficiency.
BPA schedules Hungry Horse Dam operations for power production and coordinates the
power transmission system. BPA also serves as the funding source for projects mitigating
the construction and operation of federal dams.

           U.S. Bureau of Reclamation
The Bureau of Reclamation (BOR) operates Hungry Horse Dam.

           U.S. Army Corp of Engineers
The Army Corp of Engineers (ACOE) is the regulatory entity that controls water levels
within federal Columbia River storage projects for flood control. Since the 1960s, the
agency's regulatory program's aim has been expanded to consider the full public interest in
protecting and using water resources. Section 404 of the Clean Water Act prohibits
discharging dredged or fill material into U.S. waters without a permit from the ACOE.
Because the definition of "discharge of dredged material" was modified in August 1993,
activities that impact waters, including wetlands, will most likely require an ACOE permit.

           Federal Energy Regulatory Commission
The Federal Energy Regulatory Commission (FERC) is the regulatory agency that controls
the operation of Kerr Dam.

           U.S. Fish and Wildlife Service
In addition to administering the National Bison Range and various National Wildlife
refuges and wildlife lands, the USFWS administers the Endangered Species Act as it
pertains to resident fish and wildlife. USFWS reviews and comments on land-use activities
that affect fish and wildlife resources such as timber harvest, stream alteration, dredging
and filling in wetlands and hydroelectric projects.

           U.S. Environmental Protection Agency
The United States Environmental Protection Agency (EPA) implements federal laws
designed to promote public health by protecting the nation's air, water, and soil from
harmful pollution. EPA also coordinates and supports research and anti-pollution activities
of state and local and tribal governments, private and public groups, individuals, and
educational institutions. EPA also monitors the operations of other federal agencies for



Flathead Subbasin Summary                         50                               3/6/01
their impact on the environment. The agency is responsible for implementing the Clean
Water Act, including approving Total Maximum Daily Load plans.

           Natural Resource Conservation Service
The Natural Resource Conservation Service (NRCS) provides technical support to the Soil
and Water Conservation District (SWCD) with distribution of federal cost-share monies
associated with reducing soil erosion and increasing agricultural production on privately
owned land. They provide engineering and technical support for land and water resource
development, protection, and restoration projects.

           National Park Service
The USDI National Park Service manages Glacier National Park, which incorporates
approximately 615,000 acres of the basin.

           Tribes
           Confederated Salish and Kootenai Tribes of the Flathead Indian Reservation
The Flathead Indian Reservation encompasses approximately 1.2 million acres of the basin.
Within the reservation, the tribes own approximately 662,000 acres. In addition to the
administration of their own lands, they review proposed management on public lands
within the subbasin and provide comments relative to protection of fish and wildlife
resources. Management of tribal lands is guided primarily by the tribes' Comprehensive
Resources Plan (CSKT 1994), the Flathead Reservation Forest Management Plan (CSKT
2000), the Kerr Project Fish and Wildlife Implementation Strategy (FWIS) (CSKT 2000a),
the Wetland/Riparian Habitat and Bull Trout Restoration Plan (CSKT 2000b), and the
Flathead Reservation Wetlands Conservation Plan (Price 1999). Tribal game wardens
regularly patrol the Flathead Reservation to enforce laws and regulations designed to
protect fish and wildlife.

           Tribes and State
The Flathead Lake and River Fisheries Co-Management Plan describes fisheries
management strategies and objectives for ten fish species: bull trout, westslope cutthroat
trout, lake trout, rainbow trout, kokanee salmon, yellow perch, lake whitefish, mountain
whitefish, northern pike, and largemouth bass. While the management plan addresses all
sport fish species in Flathead Lake and provides an overview of management, four other
fisheries plans specifically address, or will address, three of these species in detail: (1) the
Hungry Horse Fisheries Mitigation Implementation Plan (DosSantos, et al 1992) addresses
dam-caused losses of bull trout, westslope cutthroat trout, and kokanee salmon; (2) the
Montana Bull Trout Restoration Plan (scheduled for completion in 2000) addresses bull
trout; (3) the Bull Trout Recovery Plan (USFWS, scheduled for completion in 2001)
addresses bull trout; and (4) the FWIS addresses dam-related impacts to the fishery in
Flathead Lake. Thus, the Flathead Lake and River Fisheries Co-Management Plan serves
as an umbrella document encompassing the portions of other plans that affect, or will
affect, fish management in Flathead Lake during the 2000 to 2010 time period.



Flathead Subbasin Summary                        51                                     3/6/01
           State
           Montana Fish, Wildlife & Parks (MDFW&P)
MDFW&P is responsible for protecting and enhancing Montana's fish and wildlife and
their habitats for use and enjoyment by present and future generations. Management of the
fish and wildlife and their habitats in the subbasin is guided by MDFW&P policies and
federal and state legislation. Policies and plans that pertain to the subbasin include the
Montana Elk Management Plan (Youmans 1992), Management of Black Bears in Montana
(FWP 1994), and Management of Mountain Lions in Montana (FWP 1996). State game
wardens regularly patrol the Flathead Subbasin to enforce laws and regulations designed to
protect fish and wildlife.

           Montana Department of Natural Resources and Conservation
The Montana Department of Natural Resources and Conservation (DNRC) is responsible
for promoting the stewardship of Montana’s water, soil, forest, and rangeland resources
and for regulating forest practices and oil and gas exploration and production. The
department includes four divisions involved in land management in the subbasin. The
Conservation and Resource Development Division coordinates, supervises, and provides
financial and technical assistance to Montana’s 58 conservation districts. It also provides
technical, financial, and administrative assistance to public and private entities to complete
projects that put renewable resources to work, increase the efficiency with which natural
resources are used, or solve recognized environmental problems. The Forestry Division
protects the state’s forested and non-forested watershed lands from wildfire, provides
aviation services, operates a nursery and provides shelterbelt, windbreak, wildlife habitat
improvement, reclamation, and reforestation plantings on state and private lands. The
Forestry Division also regulates forest practices and wildfire hazards created by logging or
other forest management operations on private lands. The Trust Land Management
Division is responsible for managing the surface and mineral resources of forested,
grazing, agricultural, and other classified state trust lands to produce revenue for the benefit
of Montana’s public schools and other endowed institutions. The Water Resources
Division is responsible for many programs associated with the uses, development, and
protection of Montana’s water. Activities include interstate coordination of water issues,
centralized water rights record keeping, state water planning, dam safety regulation,
floodplain management, and drought planning.

           Montana Department of Environmental Quality
The Montana Department of Environmental Quality's mission is to protect, sustain, and
improve a clean and healthful environment throughout the state. It oversees
implementation and enforcement of the state's environmental protection laws.

           Local Government
           County Governments
County governments in the subbasin are responsible for planning and land use. They also
issue building permits.



Flathead Subbasin Summary                      52                                      3/6/01
           Flathead and Lake County Conservation Districts
Conservation districts administer the Natural Streambed and Land Preservation Act, also
known as the "310 Law." Any private individual or corporation proposing to undertake a
project or construction activity in a perennial stream must first apply for a permit from the
local conservation district. Conservation districts are the local contact for the control of
non-point source (NPS) pollution. Districts conduct projects that demonstrate NPS
pollution control practices, preferring voluntary, educational, and incentive-based
approaches to regulatory approaches. Additionally, district boards work with state and
federal regulatory agencies (for the most part, the Montana Department of Environmental
Quality and the U.S. Environmental Protection Agency) to identify problem areas and
prioritize treatment. Recently, the manner in which these problems are addressed has
become the development of Total Maximum Daily Loads for impaired streams in Montana.
Conservation districts often draw people and resources together to catalyze or assist in the
development of watershed planning efforts. Conservation districts sponsor many stream
restoration projects, conduct landowner workshops, produce and distribute informational
and educational materials, and hold demonstrations and tours of innovative riparian
management techniques and projects.

           Existing Goals, Objectives, and Strategies
The goal for the Flathead River Subbasin is to restore and protect the abundance,
productivity, and diversity of biological communities and habitats, particularly those
containing native fish and wildlife populations within the subbasin. The fish and wildlife
populations of the subbasin are of economical and cultural significance to the people of the
State of Montana, the Northwest, and the Nation and to members of the Confederated
Salish and Kootenai Tribes of the Flathead Indian Reservation.
        Our objectives are intended to address the primary limiting factors in the subbasin,
and so they follow the same grouping used for limiting factors.

           Headwaters and Associated Uplands (includes all mountain tributaries)

Objective 1       Reconnect five blocked tributaries over the next three years.
  Strategy 1.      Provide passage to migratory fish by removing potential man-caused
                   barriers, i.e. impassable culverts, hydraulic headcuts, water diversion
                   blockages, landslides, and impassable deltas.

Objective 2       Reduce fine sediments in critical spawning areas in five indexed streams
                  over the next three years.
  Strategy 1.       Maintain and protect habitat by achieving compliance with existing
                    habitat protection laws, policies, and guidelines.
  Strategy 2.       Work with the U.S. Forest Service to lower forest road densities.
  Strategy 3.       Implement stream bank stabilization measures where necessary.
  Strategy 4.       Implement riparian revegetation/rehabilitation projects.
  Strategy 5.       Agitate embedded gravels to remove silts and fine sands.
  Strategy 6.       Install artificial spawning structures where necessary.



Flathead Subbasin Summary                       53                                   3/6/01
Objective 3     Restore natural pool frequency to that of undisturbed referenced reaches
                in five streams over the next three years.
  Strategy 1.     Using Rosgen-type rehabilitation techniques, place large rocks and
                  woody debris in the stream to restore the appropriate channel
                  morphometry.

Objective 4     Eradicate or suppress non-native or hybridized populations from five
                streams over the next three years.
  Strategy 1.     Restore habitat to favor native species assemblages.
  Strategy 2.     Use RSI’s to increase native species densities in areas where natural
                  colonization is not possible.
  Strategy 3.     Protect native populations in headwater areas by installing barriers to
                  upstream invasion by non-native species. Remove barriers where the
                  threat of invasion is corrected.
  Strategy 4.     Selectively remove non-natives using effective management tools.

Objective 5     Alter 2,008 acres of forest structure and composition in the South Fork of
                the Flathead over the next three years, consistent with management and
                mitigation plans.
  Strategy 1.     Implement wildlife enhancement and protection projects in cooperation
                  with all interested parties in the subbasin as opportunities arise.

Objective 6     Acquire and/or protect key habitat parcels (endangered, threatened, and
                sensitive species habitats) through purchase, conservation easements, or
                conservation agreements to assist in maintenance of viable populations.

          Impoundments (includes Hungry Horse Reservoir, Flathead Lake, Swan Lake, and
          irrigation impoundments)

Objective 1     Reduce negative non-native species interactions in Flathead Lake and
                three irrigation impoundments over the next three years.

Objective 2     Meet the TMDL goal for reduction in phosphorus.
  Strategy 1.    Support new techniques for bank stabilization as alternatives to the
                 standard riprap material. These new techniques would serve as
                 landowner demonstration models for the reduction of sediment to the
                 mainstem and lake.
  Strategy 2.    Protect critical wetland and riparian habitats through acquisition or
                 conservation easements. Identify and rank all high priority areas and
                 establish purchase/protection mechanisms.
  Strategy 3.    Work with the Focus Watershed Coordination project to identify site-
                 specific wetland/riparian restoration projects and to coordinate with
                 landowners, agencies, and other funding sources.




Flathead Subbasin Summary                  54                                      3/6/01
Objective 3     Reduce the frequency of Hungry Horse refill failure (to within five feet of
                full pool) as compared to historic operation.
  Strategy 1.     Operate dams to provide reservoir operations that are consistent with
                  VARQ and IRC concepts by 2002.
  Strategy 3.     Reduce runoff forecasting error by increasing the number of monitoring
                  sites and improved remote-sensing technology.
  Strategy 4.     Balance the releases of stored water for flow augmentation with
                  reservoir refill. Specifically, calculate tiered flows using a conservative
                  inflow forecast, assuming the lowest 25th percentile precipitation
                  (rather than average).
  Strategy 5.     Assess cost effective means for re-vegetating the reservoir varial zone.

Objective 4     Protect, restore, and enhance riparian/wetland habitat in the upper and
                lower Flathead valleys over the next three years, meeting the annual goals
                set forth in management and mitigation plans.
  Strategy 1.     Maintain and protect habitat of native species from degradation by
                  achieving compliance with existing habitat protection laws, policies,
                  and guidelines.
  Strategy 2.     Maintain minimum flows through the purchasing and leasing of water
                  rights and water conservation agreements.
  Strategy 3.     Protect critical habitats through acquisition or conservation easements.
                  Identify and rank all high priority areas and establish
                  purchase/protection mechanisms.
  Strategy 4.     Reconnect artificially fragmented habitats.
  Strategy 5.     Work with the Focus Watershed Coordination project to identify site
                  specific restoration projects and to coordinate with landowners,
                  agencies, and other funding sources.
  Strategy 6.     Implement wildlife enhancement and protection projects in cooperation
                  with all interested parties in the subbasin as opportunities arise.

          Regulated Mainstems (includes South Fork, Upper Flathead, Lower Flathead,
          Jocko River)

Objective 1     Move Hungry Horse operations 50 percent closer to normative compared
                to current operations over the next three years.
  Strategy 1.     Implement seasonal flow windows and flow ramping rates.

Objective 2     Protect, restore, and enhance riparian/wetland habitat in the upper and
                lower Flathead valleys over the next three years, meeting the annual goals
                set forth in management and mitigation plans.
  Strategy 1.     Maintain and protect habitat of native species from degradation by
                  achieving compliance with existing habitat protection laws, policies,
                  and guidelines.




Flathead Subbasin Summary                  55                                       3/6/01
  Strategy 2.     Protect critical wetland, riparian, and associated habitats through
                  acquisition or conservation easements. Identify and rank all high
                  priority areas and establish purchase/protection mechanisms.
  Strategy 3.     Work with the Focus Watershed Coordination project to identify site-
                  specific wetland/riparian restoration projects and to coordinate with
                  landowners, agencies, and other funding sources.
  Strategy 4.     Implement wildlife enhancement and protection projects for wetland
                  and riparian areas in cooperation with all interested parties in the
                  subbasin as opportunities arise.

Objective 4     Complete an operational impact assessment and develop plans to
                mitigate for any impacts that the operations of Hungry Horse Dam may
                cause to the development and successional trends of riparian wildlife
                habitats and their associated aquatic components, in cooperation with
                ongoing fisheries mitigation activities.

Objective 5     Deal with ongoing recreation-fisheries-water quality conflicts on a daily
                basis, and educate the public to reduce these conflicts.
  Strategy 1.     Develop an education program to make boat owners aware of the
                  damage boats can do to banks because of the artificially high summer
                  lake/river levels, controlled by Hungry Horse and Kerr dams.

          Unregulated Mainstems (includes North Fork, Middle Fork, and Swan Rivers)

Objective 1     Treat all sites that have occurrences of purple loosestrife or Eurasian
                water milfoil.

Objective 2     Protect, restore, and enhance riparian/wetland habitat in the upper and
                lower Flathead valleys over the next three years, meeting the annual goals
                set forth in management and mitigation plans.
  Strategy 1.     Maintain and protect habitat of native species from degradation by
                  achieving compliance with existing habitat protection laws, policies,
                  and guidelines.
  Strategy 2.     Protect critical wetland and riparian habitats through acquisition or
                  conservation easements. Identify and rank all high priority areas and
                  establish purchase/protection mechanisms.
  Strategy 3.     Work with the Focus Watershed Coordination project to identify site-
                  specific wetland/riparian restoration projects and to coordinate with
                  landowners, agencies, and other funding sources.
  Strategy 4.     Implement wildlife enhancement and protection projects for wetland
                  and riparian areas in cooperation with all interested parties in the
                  subbasin as opportunities arise.

Objective 3     Deal with ongoing human/wildlife conflicts on a daily basis, and educate
                the public to reduce human/wildlife conflicts.


Flathead Subbasin Summary                  56                                       3/6/01
  Strategy 1.     Decommission unnecessary roads to reduce harassment of wildlife and
                  encourage more uniform use of available wildlife habitat.
  Strategy 2.     Continue to develop and implement strategies to educate private
                  landowners on how to coexist with wildlife and preserve or enhance
                  habitat.
  Strategy 3.     Educate anglers about native fish issues, fishing regulations, and proper
                  identification of native species.

          Valley Tributaries & Wetlands (includes all valley tributaries and the Whitefish and
          Stillwater rivers)

Objective 1     Eliminate three sources of non-native or hybridized fish populations over
                the next three years.
  Strategy 1.     Selectively remove populations using effective management tools (i.e.
                  chemical treatment, intensive electrofishing, installation of fish
                  migration barriers etc.).

Objective 2     Protect, restore, and enhance riparian/wetland habitat in the upper and
                lower Flathead valleys over the next three years, meeting the annual goals
                set forth in management and mitigation plans.
  Strategy 1.     Maintain and protect habitat of native species from degradation by
                  achieving compliance with existing habitat protection laws, policies,
                  and guidelines.
  Strategy 2.     Protect critical wetland and riparian habitats through acquisition or
                  conservation easements. Identify and rank all high priority areas and
                  establish purchase/protection mechanisms.
  Strategy 3.     Work with the Focus Watershed Coordination project to identify site-
                  specific wetland/riparian restoration projects and to coordinate with
                  landowners, agencies, and other funding sources.
  Strategy 4.     Implement wildlife enhancement and protection projects for wetland
                  and riparian areas in cooperation with all interested parties in the
                  subbasin as opportunities arise.

Objective 3     Significantly reduce the level of sedimentation in five impacted spawning
                areas over the next three years.
  Strategy 1. Restore normative surface-water runoff patterns in upland areas using the
                  best management practices and habitat improvement measures (i.e.
                  culvert removal and replacement, sediment source abatement, road
                  obliteration, and re-vegetation).
  Strategy 2. Restore natural stream channel function and form using soft methods (i.e.
                  bank stabilization, streambank and riparian re-vegetation, riparian
                  fencing, in-stream channel habitat structures).

Objective 4     Maintain temperatures within the tolerance range of native fish species.



Flathead Subbasin Summary                    57                                       3/6/01
  Strategy 1.     Deploy continuous recording thermographs in important tributaries to
                  monitor water temperatures in relation to tolerance range of native fish
                  species.
  Strategy 2.     Improve riparian and in-stream habitat using stream channel and
                  riparian habitat restoration methods (Rosgen 1995).

Objective 5     Deal with ongoing human/wildlife conflicts on a daily basis, and educate
                the public to reduce human/wildlife conflicts.
  Strategy 1.     Decommission unnecessary roads to reduce harassment of wildlife and
                  encourage more uniform use of available wildlife habitat.
  Strategy 2.     Continue to develop and implement strategies to educate private
                  landowners on how to coexist with wildlife and preserve or enhance
                  habitat.
  Strategy 3.     Educate anglers about native fish issues, fishing regulations, and proper
                  identification of native species.

Objective 6     Develop a reintroduction plan for Columbian sharp-tailed grouse in the
                Flathead Basin.
  Strategy 1.     Work with private, tribal, state, and federal landowners to identify
                  opportunities to restore Columbian sharp-tailed habitat and
                  populations.

          Lakes (includes connected and closed-basin lakes)

Objective 1     Remove the sources of non-native or hybridized trout from two to three
                connected lakes each year over the next three years.
  Strategy 1.     Selectively remove non-desirable fish and restock with native desirable
                  fish.
  Strategy 2.     Establish barriers to non-native fish escapement or spawning.


Objective 2     Deal with ongoing human/wildlife conflicts on a daily basis, and educate
                the public to reduce human/wildlife conflicts.
  Strategy 1.     Decommission unnecessary roads to reduce harassment of wildlife and
                  encourage more uniform use of available wildlife habitat.
  Strategy 2.     Continue to develop and implement strategies to educate private
                  landowners on how to coexist with wildlife and preserve or enhance
                  habitat.
  Strategy 3.     Educate anglers about native fish issues, fishing regulations, and proper
                  identification of native species.

Objective 3     Protect, restore, and enhance riparian/wetland habitat in the upper and
                lower Flathead valleys over the next three years, meeting the annual goals
                set forth in management and mitigation plans.




Flathead Subbasin Summary                  58                                      3/6/01
  Strategy 1.       Maintain and protect habitat of native species from degradation by
                    achieving compliance with existing habitat protection laws, policies,
                    and guidelines.
  Strategy 2.       Protect critical wetland and riparian habitats through acquisition or
                    conservation easements. Identify and rank all high priority areas and
                    establish purchase/protection mechanisms.
  Strategy 3.       Work with the Focus Watershed Coordination project to identify site-
                    specific wetland/riparian restoration projects and to coordinate with
                    landowners, agencies, and other funding sources.
  Strategy 4.       Implement wildlife enhancement and protection projects for wetland
                    and riparian areas in cooperation with all interested parties in the
                    subbasin as opportunities arise.

Objective 4       Maintain the trophic status of all classified lakes.
  Strategy 1.      Restore physical integrity of degraded habitat where logistically and
                   technically feasible.
  Strategy 2.      Achieve compliance with water quality standards and develop TMDLs
                   for water quality impaired streams (streams listed on the DEQ 303(d)
                   impaired water bodies list) that are priority native species habitat.

Objective 5       Increase the angler opportunities in three closed-basin lakes over the next
                  three years.
  Strategy 1.       Utilize hatchery production to stock offsite, closed-basin lakes.
  Strategy 2.       Where appropriate, rehabilitate three closed-basin lakes per year to
                    provide maximum angler opportunity and system productivity.
  Strategy 3.       Form partnerships with the public through the Focus Watershed
                    Program and other avenues to increase awareness of the role of
                    mitigation in achieving native species and habitat restoration.

           Research, Monitoring, and Evaluation Activities
Monitoring and evaluation activities will occur concurrently with on-the-ground BPA-
funded projects described in the section titled Existing and Past Effort. Monitoring will
include project-specific and watershed-level parameters. Specific monitoring strategies,
including pre- and post-treatment sampling, has been designed for each completed and
ongoing project (generally the strategies involve site-specific measures, photo points, and
migrant trapping). These activities are combined with watershed level, long-term, time-
series indices for habitat and fish populations to evaluate direct and indirect effects of
projects. This extensive monitoring program is maintained through a cooperative effort
with other agencies.
        Specific ongoing monitoring activities are listed below:

           Fisheries

MDFW&P will conduct the following BPA-funded fisheries monitoring activities:



Flathead Subbasin Summary                    59                                      3/6/01
      To develop habitat suitability use curves required by the Instream Flow Incremental
       Methodology (IFIM) Project (BPA #9502500) on the Flathead River, MDFW&P
       will collect micro- and macro-habitat parameters (i.e. depth, velocity, substrate,
       habitat type etc.) for use in developing weighted useable area curves for size-classes
       of bull trout and westslope cutthroat trout.

      To monitor effects of selective withdrawal at Hungry Horse Dam on the Flathead
       River ecosystem, MDFW&P will monitor river temperatures at six locations in the
       Flathead River system; quantify differences in macrozoobenthos diversity and
       abundance and pre- and post-selective withdrawal; and quantify and compare
       whitefish growth rates pre and post.

      To assess abundance, distribution, and food habits of predator fish species (lake
       trout, northern pike) in the mainstem, North, and Middle forks of the Flathead
       River, MDFW&P will perform creel surveys throughout the Flathead River system;
       obtain growth information and analyze stomach contents from harvested northern
       pike and lake trout; and tag and release fish for abundance and distribution
       analyses.

      To assess distribution and movements of juvenile, sub-adult, and adult bull trout
       and westslope cutthroat trout in the mainstem, North, and Middle forks of the
       Flathead River, MDFW&P will use radio-telemetry to collect data on bull trout
       distribution, movement, and habitat use through weekly ground, boat, and aerial
       surveys.

      To assess distribution and movements of westslope cutthroat trout, rainbow trout,
       and WCT x RBT hybrids in the mainstem, North, and Middle forks of the Flathead
       River, MDFW&P will collect data on westslope cutthroat trout distribution,
       movement, and habitat use through weekly ground, boat, and aerial surveys.

      To monitor watershed level fish and habitat parameters in cooperation with fish
       management staff and other BPA projects, MDFW&P will annually: monitor
       spawning, incubation and habitat quality by McNeil method of streambed coring in
       33 tributaries (to assess juvenile bull trout rearing habitat quality) and by substrate
       scoring in 21 tributaries; conduct annual migratory cutthroat and bull trout redd
       counts in 45 index tributary reaches to monitor adult runs; conduct annual cutthroat
       and bull trout juvenile estimates in 31 tributaries to monitor recruitment; conduct
       river population estimates in mainstem and forks of Flathead River; conduct annual
       gill net series on Flathead Lake and Hungry Horse Reservoir; and collect disease
       samples from wild fish populations.

      MDFW&P will evaluate past mitigation projects on Taylor's Spring Creek, Hay
       Creek, Dayton Creek and monitor fish growth, species composition, and angler use
       at past lake rehabilitations on Lion, Rogers, Bootjack, Murray, and Dollar lakes


Flathead Subbasin Summary                    60                                       3/6/01
       plus other offsite fish-plant waters. A specific monitoring strategy, including pre-
       and post-treatment sampling, is designed for each restoration project. These are
       combined with watershed level spawning substrate and redd counts, electrofishing,
       and gillnet monitoring series to assess direct and indirect effects of the program.

      MDFW&P will assess the timing and magnitude of discharge releases (e.g. ramping
       rates and flow regimes) from Hungry Horse Dam as related to the distribution,
       habitat use and movements of juvenile and adult bull trout and westslope cutthroat
       trout.

      MDFW&P will quantify impacts of flow releases from Hungry Horse Dam on the
       macroinvertebrate community structure and temporal frequency dynamics of
       trophically important benthic species in the Flathead River downstream of Hungry
       Horse Dam.

      MDFW&P will conduct research on an as needed basis as specified in the USFWS
       Biological Opinion on bull trout in the upper Flathead River system.

CSKT will conduct the following BPA-funded fisheries monitoring activities:

      Native species abundance in Flathead Lake will be monitored using spring
       gillnetting.

      The biology of lake trout in Flathead Lake will be monitored using fall gillnetting.

      The success of offsite fish plants will be monitored through creel surveys and fish
       sampling.

      Exploitation rates of sport fish in Flathead Lake will be monitored using a year-long
       creel survey.

      The Watershed Focus Coordinator's effectiveness will be monitored by tracking the
       number of individuals in the sub-watershed participating in restoration activities.

In addition, CSKT Fisheries and Water Management programs will monitor:

      Native fish populations on a 10-year cycle to evaluate long-term viability based on
       the BayVam or similar model by measuring abundance, available habitat, and year-
       class distribution.
      Substrate condition by McNeil coring or substrate embeddedness in all streams on a
       15-year cycle.
      Channel complexity in all streams on a 15-year cycle.
      Streams by maintaining and intermittently reporting results for the reservation-wide
       Stream Assessment and Reference-reach Assessment Monitoring Program.



Flathead Subbasin Summary                   61                                      3/6/01
      Timber sales, which include (for each sale): sediment source surveys, BMPs
       implementation and road abandonment, cumulative effects, stream and wetlands
       inventories, and forest-wide stream-reach assessment surveys for 16 reaches.

BPA-funded fisheries research includes the following projects:

      In 1999, Montana initiated a modified Instream Flow Incremental Methodology
       (IFIM) project on the Flathead River to refine the river component of HRMOD. The
       project has been approved for two years of funding and the final year, FY2000, is
       pending NWPPC approval. The IFIM research will calibrate simulations of
       hydraulic conditions (stage/discharge and velocities etc.), and fish habitat from
       Hungry Horse Dam to Flathead Lake at various discharges from Hungry Horse
       Dam. An optimization program is scheduled for development to allow managers to
       assess tradeoffs between the requirements of reservoir and riverine biota, when
       conflicts occur between reservoir operation and river flow limits as per the
       MDFW&P. MDFW&P and CSKT monitor the effects of dam operation in Hungry
       Horse Reservoir and the Flathead River and its tributaries.

      Factors controlling mysis abundance in Flathead Lake will be researched by CSKT
       through biweekly mysis sampling with associated limnological parameters.

           Wildlife
BPA-funded wildlife projects have been undertaken by MDFW&P. BPA-funded wildlife
project monitoring has provided, and continues to provide, important information to insure
that mitigation is being carried out in the most biologically sound and economically
efficient way possible. Only limited funding has been available for wildlife projects in the
lower portion of the basin.

          A non-game monitoring program by MDFW&P will evaluate the effects of
           habitat enhancements at Hungry Horse on breeding-bird communities to
           determine if enhancement prescriptions for big game species effectively restore
           habitat for bird species as well. Non-game birds are widely recognized as one of
           the best indicators of habitat quality. They inhabited all the habitats lost in the
           project area. In addition, there is growing international concern over the status
           and trend in many western bird populations and their relationships with habitat
           management practices. In order to optimize benefits to all wildlife, monitoring
           needs to determine whether activities done to benefit big game animals also
           benefit other species groups that depend on those habitats. A final summary
           report of this eight-year effort will be prepared by June 2001. The results will be
           used to review and develop new habitat enhancement proposals and methods
           for measuring wildlife benefits.

          Big game monitoring will evaluate the effectiveness of big game habitat
           enhancements along Hungry Horse Reservoir. Vegetation monitoring is
           conducted at a representative sample of paired treatment and control areas to


Flathead Subbasin Summary                    62                                      3/6/01
           document changes that result from each of the various treatments. Key
           vegetation components such as density, species composition, canopy coverage
           and vigor of forage plants will be measured. The elk monitoring portion of this
           project was originally designed to determine the magnitude of elk population
           increases resulting from habitat enhancements. However, given the results of
           Stansberry (1996) this goal will be re-evaluated. A final summary report of this
           13-year effort will be prepared by June 2001. The results will be used to review
           and develop new habitat enhancement proposals and methods for measuring
           wildlife benefits.

          MDFW&P conducts annual population monitoring on big game, furbearer, and
           non-game populations in the subbasin through a variety of surveys and
           inventories. MDFW&P conducts annual surveys of elk, mule deer, white-tailed
           deer, moose, mountain goats, and grizzly bears. MDFW&P also conducts
           breeding bird surveys on each of their wildlife management areas as well as
           furbearer track surveys during winter.

          The Montana Bald Eagle Working Group and the Montana Loon Society
           coordinate annual bald eagle and common loon occupancy and productivity
           surveys. The National Audubon Society sponsors annual Christmas bird counts.
           The U.S. Fish and Wildlife Service coordinates annual breeding bird surveys in
           the Flathead Subbasin as part of the national surveys. There are also MAPS
           (Monitoring Avian Production and Survivorship) stations conducted each year,
           an effort coordinated by the Point Reyes Bird Observatory in California.

As part of its management program, the CSKT Wildlife Management Program monitors:

      Wildlife populations on the Flathead Indian Reservation and in adjacent habitats.
       Big game, waterfowl, upland gamebirds, endangered, threatened and sensitive
       species, non-game species, furbearers, amphibians, and reptiles are routinely
       monitored.

      Recovery of endangered and threatened species by continuing to monitor
       populations in coordination with other state and federal agencies. The tribes have
       also taken a lead to reintroduce peregrine falcons and trumpeter swans. Other
       reintroduction plans involve Columbian sharp-tailed grouse and northern leopard
       frogs.

      Activities prescribed to eliminate or mitigate the impacts of proposed human
       activities, including forest management, range management, construction, and a
       wide variety of other projects.

Research includes the following projects:




Flathead Subbasin Summary                   63                                     3/6/01
       Long-term black bear research is being conducted to improve harvest criteria used
        for management by assessing the vital rates (reproduction and mortality) of a
        typical black bear population in Swan River Valley. The project is also
        documenting local population size, trend, and sustainable harvest level estimates.
        Simultaneously, the project will develop estimates of black bear population size in
        typical hunting areas throughout western and central Montana to estimate current
        harvest rates.

       Long-term monitoring and associated research on the Flathead Indian Reservation
        includes work on bald eagles, small mammal population dynamics and their
        impacts upon other species, grizzly bears, amphibians, and forest carnivores.



           Statement of Fish and Wildlife Needs
The following near-term priority fish and wildlife needs have been identified for the
Flathead River Subbasin:

   Protect habitat of native fish and wildlife populations.
    There is an extreme need to use land acquisitions and conservation easements to protect
    significant intact habitats that support rare, unique, or highly productive populations of
    fish and wildlife or that are important for sustaining annual public harvests. More
    active management of existing fish and wildlife management areas is also needed to
    provide increased benefits.

   Reduce or eliminate hybridization and competition with non-native species.
    Hybridized fish populations in headwater lakes and connected streams pose a threat to
    genetically pure westslope cutthroat populations. Illegal introductions of non-native
    fish species have likewise impacted progress toward fisheries mitigation and native
    species recovery. Rehabilitation of selected lakes is needed to create genetic reserves
    for native fish, prevent genetic introgression, improve fisheries, and eliminate source
    populations for further illegal introductions. Rehabilitation of selected interconnected
    streams in the upper Flathead River system is needed to prevent genetic introgression,
    improve fisheries, and suppress or eradicate hybridized or pure rainbow source
    populations. Public awareness of damages caused by illegal fish introductions must be
    a priority. Existing laws regulating the transport of live fish must be enforced. There is
    a need to reduce or eliminate non-native predator fish species—for example lake trout
    and northern pike— that pose a threat to the persistence of native fish populations in
    the river/lake system. Various techniques should be implemented to assess the
    distribution, abundance, and food habits of these non-native predators in the Flathead
    system upstream of Kerr Dam.

    There is a need to reduce or eliminate non-native species—for example, purple
    loosestrife, Eurasian water milfoil, spotted knapweed, leafy spurge, and bull frogs—
    that pose a threat to wildlife populations and aquatic organisms.



Flathead Subbasin Summary                     64                                       3/6/01
   Restore locally extirpated fish and wildlife species to a self-sustaining condition.
    Self-supporting fish populations need to be reestablished in areas where their habitat
    can be restored. Natural colonization of restored habitats would be encouraged where
    possible. Where wild stocks have been extirpated, an appropriate source population
    could be replicated through imprint planting of genetically compatible eyed eggs or fry.
    Various techniques for reestablishing wild runs need to be evaluated through rigorous
    comparisons of effectiveness and risk.

    Wherever habitat is available or where there is a potential for habitat restoration, there is
    a need to restore populations (and habitats) of native wildlife species with populations
    that have been extirpated or drastically reduced (for example trumpeter swans, northern
    leopard frogs, Columbian sharp-tailed grouse, and burrowing owls).

   Reconnect fragmented habitats and isolated populations.
    There is a need to reconnect access to spawning and rearing habitat that has been
    blocked by human-caused barriers. Improving fish passage into existing habitat is a
    cost-effective tool to replace habitat lost during the construction and operation of the
    hydropower system. These efforts will be consistent with the maintenance of genetic
    integrity in fish species and protection of threatened, endangered, and senstive plant
    and animal species.
        For wildlife there is a need to reconnect fragmented habitats and protect existing
    migration corridors and existing connected habitats from additional fragmentation. This
    can be accomplished by working with local communities to modify activities such as
    timber harvesting, housing developments, and road construction and by acquiring key
    parcels of land and establishing conservation easements with landowners. In addition,
    the need to acquire and manage key habitat parcels is an extremely high priority,
    especially on the Flathead Indian Reservation.

   Restore in-channel habitat structure, function, and complexity.
    Fish require suitable habitats for natural production and survival through all life stages.
    Sediment sources need to be reduced or eliminated. Fine sediments accumulating in
    spawning substrate reduce egg to fry survival such that natural reproduction may be of
    insufficeint quanity to fully seed available rearing habitat with juevenile fish. Pools
    and rearing habitat clogged with sediment need to be restored to improve the
    productive capacity of the stream. Land management needs to be consistent with
    natural stream function. Possible treatments include stream bank stabilization, livestock
    fencing, sediment source abatement, riparian re-vegetation, upland road improvement
    or obliteration, surface water drainage improvements, and agitation of embedded
    gravels to remove silts and fine sands. In some locations the installation of artificial
    spawning structures may be beneficial. Stream habitats on channelized or impacted
    streams need to be restored to natural form and function. This can be accomplished
    passively or by restoring the stream to a stable channel form. Stream rehabitlitation
    measures may include placing large rocks, woody debris, and bank stabilization
    structures in the stream to restore the appropriate channel morphometry. Similarly,



Flathead Subbasin Summary                      65                                        3/6/01
    lake or reservoir habitat needs be improved by re-vegetating areas subject to water
    fluctuations or by adding wooden cribs, slash structures, or artifical substrates.

   Restore riparian and wetland habitats and floodplain function
    Riparian and wetland areas have the greatest influence over the biological health of the
    watershed. They provide security cover for fish and terrestrial wildlife, habitat and food
    for insect production, and woody debris that creates channel diversity and pocket water
    for spawning gravel deposition. The canopy of the riparian zone helps maintain cool
    water temperatures and traps sediments produced from adjacent land areas. There is a
    need to identify and protect the best available remaining riparian and wetland habitats
    through the use of conservation agreements and land acquisitions and a need to modify
    the activities that are causing the degradation of impacted areas or that are preventing
    the ecosystem from recovering. Riparian and wetland vegetation needs to be restored
    and protected through fencing and re-vegetation projects.
        Channelization, road fill, bank armoring, and other encroachments along stream
    segments have narrowed channels and limited meanders inside floodplains, which has
    created shorter channels, steeper gradients, higher velocities, a loss of storage and
    recharge capacity, bed armoring, and entrenchment. Restoration of highly altered
    stream reaches and protection of intact systems is needed to restore and maintain
    stream diversity.

   Restore watershed function and condition
    In terrestrial habitats, fire exclusion, logging practices and agriculture has created many
    changes since pre-European times. Forests have expanded onto grasslands, overall
    diversity has declined, and the species composition has shifted. Forest structures have
    changed, and there have been increases in the density of forest vegetation. Changes in
    patch size and edge, shifts in the ages and sizes of trees, and increases in road densities
    have also occurred. All these trends have resulted in less resilient and less diverse
    habitats for fish and wildlife. There is a need to reverse these trends by changing forest
    and agricultural practices so vegetation communities become more diverse and
    sustainable and less vulnerable to catastrophic fires and epidemic insect and disease
    outbreaks. There is a need to use mechanical treatments focused not on commodity
    production but on restoration in combination with prescribed fire to restore and
    maintain forest and grassland communities and to enhance fish and wildlife habitats.
    There is also a need to identify and protect the best available remaining habitats
    through the use of conservation agreements and land acquisitions.

   Reduce point and non-point sources of pollution
    There is a need to address all significant point and non-point sources of water pollution
    in the system. Reductions in water quality can lower the overall resilience of aquatic
    environment and keep fish and wildlife populations from recovering. Standards for
    total maximum loading of nutrients (TMDL), thermal pollution, and gas saturation
    need to be enforced.




Flathead Subbasin Summary                     66                                       3/6/01
   Restore the quantity, seasonal pattern, and stability of streamflows and reservoir
    conditions.
    There is a need to operate dams to restore and maintain normative hydrologic
    conditions (conditions that mimic natural processes and minimize impacts on fish and
    wildlife). Dams need to be operated to provide reservoir operations consistent with
    VARQ and IRC concepts. Specifically, there is a need for a gradual ramp-down
    approach to Flathead River flows after the spring runoff and a need to maintain stable
    discharges during the biologically productive summer months in order to benefit native
    species. There is also a need to address downstream operational impacts of Hungry
    Horse Dam upon riparian habitat on the Flathead River both upstream and downstream
    of Flathead Lake.

   Replace lost tribal hunting, fishing, and gathering areas and cultural and spiritual
    sites.
    Construction of Hungry Horse Dam inundated 23,750 acres of wildlife habitat in the
    South Fork of the Flathead River. This habitat was located primarily on federal lands
    administered by the U. S. Forest Service. As a source of resources for subsistence under
    the language of the Hellgate Treaty of 1855, these habitats were very important to
    members of the Salish and Kootenai Tribes. With inundation, all of these lands and the
    resources that they produced were lost to use forever by the tribes. In 1990, the State of
    Montana and BPA signed a wildlife settlement agreement to mitigate for inundation
    losses related to Hungry Horse Dam. The CSKT were not signatory to this agreement
    and were not included in the negotiations that led to its development. The CSKT have
    been a participant in the Montana Wildlife Mitigation Advisory Committee, which
    advises the MDFW&P on proposed mitigation projects. Although some projects have
    had benefits for wildlife resources that tribal members utilize, most have not served to
    adequately replace the wildlife and wildlife habitat losses that occurred.
         As a result, a substantial deficit in mitigation of inundation losses continues. There
    is a need to acquire off-site habitat similar to that degraded or destroyed by Hungry
    Horse construction and a need to enhance or restore acquired habitat to maximize
    wildlife productivity. Specifically, there is a need to: (1) secure important spring and
    fall grizzly bear habitats along the Mission Front and Rattlesnake Mountains from
    further habitat fragmentation and high disturbance levels; (2) secure and enhance big
    game winter ranges at key areas on the reservation; (3) mitigate for ongoing impacts of
    Hungry Horse Dam on the habitat quality and quantity of the lower Flathead River; (4)
    preserve, protect, and restore remaining acres of unprotected wetland habitat and
    associated grasslands in the Ninepipe-Kicking Horse area; and (5) restore native
    grassland and woody draw habitats that have been heavily impacted by livestock use
    and that no longer support the wildlife species that they did historically.




Flathead Subbasin Summary                     67                                      3/6/01
   Reduce human/wildlife conflicts.
    There is a need for increased public outreach and education and law enforcement to
    reduce human/wildlife conflicts resulting from high rates of rural residential growth.
    Effective educational strategies must be developed to educate homeowners about how
    to coexist with wildlife. The need for continued law enforcement is integral to fish and
    wildlife species and habitat protection in the subbasin, as are forest road closures,
    obliteration, and other road treatments in order to minimize poaching and harassment
    and to reclaim habitat. There is a need to limit new development of forest habitats to
    avoid further losses and intensified human/wildlife conflicts. There is also a need to
    improve winter and year-round fish and wildlife habitat on county, private, and federal
    forest lands.


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   westslope cutthroat trout fry from varying substrate compositions in a natural stream
   channel. North American Journal Fisheries Management 13:817-822.
Weaver, T. M., J. J. Fraley, and P. J. Graham. 1983. Fish and habitat inventory of streams
   in the Middle Fork of the Flathead River. Flathead River Basin Environmental Impact
   Study. Prepared for Montana Fish, Wildlife & Parks, Kalispell...
Werner, J.K., T. Plummer, and J. Weaselhead. 1995. Amphibians and reptiles of the
   Flathead Indian Reservation. Confederated Salish and Kootenai Tribes, Pablo, MT.
Werner, J.K., T. Plummer, and J. Weaselhead. 1998. Amphibians and reptiles of the
   Flathead Indian Reservation. Intermountain Journal of Science: 4:33-49.
Wood, M. A. 1991. Columbian Sharp-tailed Grouse Mitigation Implementation Plan for
   Western Montana. Montana Fish, Wildlife & Parks. 24pp.
Youmans. 1992. Montana Elk Management Plan Management, Montana Fish, Wildlife &
   Parks, Kalispell, MT
Zackheim, H. 1983. Final report of the steering committee for the Flathead River Basin
    Environmental Impact Study. Funded by EPA under grant number R00822201,
    Kalispell, Montana, USA.
Zollweg, E. C. 1998. Piscine predation on bull trout in the Flathead River, Montana.
    Master’s Thesis, Montana State University, Bozeman, Montana. 97 pp.
Zubik, R. J. and J. J. Fraley. 1987. Determination of fishery losses in the Flathead
    system resulting from the construction of Hungry Horse Dam. Prepared for
    Bonneville Power Administration, Portland, Oregon by Montana Fish, Wildlife &
    Parks, Kalispell, Montana.




Flathead Subbasin Summary                   74                                     3/6/01
           Subbasin Recommendations

           FY 2001 Projects Proposals Review
The following subbasin proposals were reviewed by the Subbasin Team and the Province
Budget Work Group and are recommended for Bonneville Power Administration project
funding for the next three years.
    Please note that the fish habitat and focus watershed components of project number
24018 are parts of ongoing BPA-funded projects (9101901: Hungry Horse Fisheries
Mitigation - Flathead Lake and 199608701: Focus Watershed Coordination-Flathead River
Watershed, respectively). Similarly, the fisheries component of project 24019 continues the
parts of project 9101901 that are not included in 24018.
    Table 1 provides a summary of how each project relates to resource needs, management
goals, objectives and strategies, and other activities in the subbasin.

           Projects and Budgets


           Continuation of Ongoing Projects


Project: 199101903 – Hungry Horse Mitigation

           Sponsor: Montana Fish, Wildlife & Parks (MFWP)
           Short Description:
Mitigation for the construction and operation of Hungry Horse Dam (HHD). Implements
habitat restoration, improves fish passage, protects and recovers native fish populations,
and reestablishes fish harvest opportunities.
           Abbreviated Abstract
Hungry Horse Dam, completed in 1952, impounded the South Fork of the Flathead River
creating the 30-mile Hungry Horse Reservoir. Research to quantify the biological impacts
caused by dam construction and operation began during the late1970s. In 1993, the
Northwest Power Planning Council adopted the Hungry Horse Dam Fisheries Mitigation
Implementation Plan. This plan contains an approved loss statement quantifying fish and
habitat that was impacted by the construction and operation of Hungry Horse Dam and
describes specific measures to protect and enhance resident fish and aquatic habitat.
Installation of a selective withdrawal device at Hungry Horse Dam successfully restored
normative temperatures to the Flathead River in 1996. Empirically calibrated computer
models were developed to establish dam operations to benefit biological productivity in the
reservoir and river system. Reservoir operating requirements were published in 1996 and
updated in 1999. Research on the Flathead River is quantifying the influence of regulated
flow and temperature on native fish with special emphasis on risks posed by non-native
fish species. Basin-wide genetic surveys, migrant trapping, and radio-telemetry studies
have identified streams where hybridization is occurring between native westslope
cutthroat trout and non-native rainbow trout; results are being used to protect native stocks.
A Flathead Basin habitat and fish passage plan was updated in 1997 that guides our


Flathead Subbasin Summary                     75                                      3/6/01
watershed restoration efforts. Fish passage projects reconnect access to blocked spawning
and rearing habitat. Habitat projects in stream, lake, and reservoir environments emphasize
passive restoration with conventional, biotechnical, and experimental approaches. Offsite
projects, particularly lake rehabilitations, have been successful in creating genetic reserves
for native fish, drastically improving fisheries, and/or eliminating source populations for
further illegal fish introductions. A specific monitoring strategy, including pre- and post-
treatment sampling, is designed for each restoration action to improve cost effectiveness.

            Relationship to Other Projects
Results of many of our efforts are applicable to other programs in the Columbia River
basin. Biotechnical approaches to stream habitat and riparian restoration have contributed
knowledge of vegetative bank-stabilization techniques. Projects also include novel or
experimental approaches with wide applicability. Examples include a step-pool fish ladder
completed with low-cost, natural materials and development of the Integrated Rule Curves
(IRCs) for dam operation to enhance fish and wildlife mitigation. IRCs are being
developed for other storage projects in the Columbia Basin. The ISG and ISAB stated that
the IRCs are consistent with the normative river concept and provide a tool for assessing
tradeoffs between reservoir and river requirements. They recommended that IRCs be
applied to other Columbia River sub-basins. Tools for decision making are especially
important now that many Columbia Basin fish species have been listed or proposed for
listing under ESA. Changes in dam operation for recovery of lower Columbia River fish
stocks have been shown to impact resident fish in the headwaters (ISAB 1997) and must be
balanced to benefit all native species. Recent changes to dam operation called for in the
2000 Biological Opinion on bull trout and listed anadromous species provide a better
balance.

      Project ID                       Title                      Nature of Relationship
199502510                 Instream Flow Incremental        Physical and hydraulic
                          Methodology (IFIM) study         component of the IFIM model
                          on the Flathead River
19101901                  Hungry Horse Mitigation -        Partner with CSKT in mitigation
                          Flathead Lake and Habitat        for Hungry Horse
                          Enhancement (CSKT)
199608701                 Focus Watershed                  Cooperator in Dayton Creek
                          Coordination - Flathead          restoration
                          Basin (CSKT)
3874700                   Streamnet Geographic             Provide GIS and GPS support.
                          Information Services unit        Design and archive watershed
                                                           maps


            Relationship to Existing Goals, Objectives and Strategies
Section 10.3A of the FWP details Hungry Horse resident fish mitigation. Measures
10.3A.11 & 10.3A.12 direct MFWP to implement habitat enhancement projects described
in the Mitigation and Implementation Plans. The approved Implementation Plan, which
includes fish and habitat loss statements, decision trees, and project prioritization criteria



Flathead Subbasin Summary                          76                                        3/6/01
and rationale is a guiding framework for this program. In approving this plan, the NPPC
and Independent Scientific Group encouraged "implementation of habitat improvement
projects as a high priority." Montana's Fisheries Mitigation Guidelines also stress "natural
fish reproduction and habitat whenever possible." Our goal is to mitigate documented
losses of native fish through habitat enhancement, fish passage improvements, and
improved dam operation. The Flathead Subbasin contains some of the last and best
remaining strongholds for bull trout and westslope cutthroat trout.
        Measures 903(a) and (b) of the 1987 FWP placed the 85-foot drawdown limit at
HHD for power purposes and directed BPA to fund restoration of fish losses when the
drawdown limit is exceeded. These limits remain in effect until the IRCs are implemented
(measure 10.3A.3, 10.3A.7 and 10.3A.8, NPPC 1995). Measure 10.3A.4 directs MFWP to
continue to refine the IRCs. The IFIM project (directed by 10.3A.18) will help refine the
riverine aspects of the IRCs and provide information for consultations between MFWP,
CSKT and ACOE (10.3A.9) for decision making when a conflict occurs between
maintaining minimum flows (10.3A.1) and maintaining reservoir levels (10.3A.3).
Measures 10.3A.6-8 direct BPA and ACOE to fund studies to evaluate HHD operations on
fish and repair of fish losses when the IRCs are violated for power or flood control.
        The project supports Flathead Subbasin Summary objectives to improve fish
passage, restore habitats in stream, lake, and reservoir environments, create genetic
reserves for native fish, and eliminate source populations for further illegal fish
introductions.

             Review Comments
No provincial review comments.

             Budget
             FY02                                  FY03                        FY04
$982,850                            $990,000                      $1,065,000
Category: High Priority             Category: High Priority       Category: High Priority




Project: 199101904 – Stocking of offsite waters for Hungry Horse Mitigation - Creston
National Fish Hatchery
             Sponsor: U.S. Fish and Wildlife Service (USFWS)
             Short Description:
Produce hatchery fish for offsite stocking to mitigate losses to Flathead Lake caused by
construction and operation of Hungry Horse Dam.
             Abbreviated Abstract
We employ hatchery fish production of up to 100,000 westslope cutthroat trout and
100,000 rainbow trout to mitigate for Hungry Horse Dam hydro-related losses of 415,000
salmonids annually from Flathead Lake. In order to partially offset lost angler opportunity,
this project creates new recreational fishing opportunities, reduces pressure on native



Flathead Subbasin Summary                          77                                  3/6/01
stocks. Hatchery fish are stocked annually into small offsite closed-basin lakes within the
Flathead Basin.

             Relationship to Other Projects
      Project ID                       Title                          Nature of Relationship
199101901                  Flathead Lake Monitoring and       All projects are under Hungry Horse
                           Habitat Enhancement                Fisheries Mitigation umbrella, the
199101903                  Hungry Horse Mitigation-           goal of which is to restore and protect
                           Watershed Restoration and          the abundance, productivity, and
                           Monitoring                         diversity of biological communities
199101002                  Flathead River Native Species      and habitats in the Flathead River
                           Project                            Subbasin.
199502500                  Flathead River Instream Flow       This project aims to provide angler
                           Project                            opportunities in smaller,
199608701                  Focus Watershed                    reclaimed, closed-basin lakes, and
                           Coordination-Flathead River        reduce pressure on mainstem
                           Watershed                          waters while habitat enhancements
                                                              and population studies are conducted
                                                              through the related projects.


             Relationship to Existing Goals, Objectives and Strategies
This proposal represents a continuing effort to satisfy a portion of the Hungry Horse Dam
loss statement approved by the NWPPC in 1991under amendment 903(h). It also follows
directives of the 1994 Fish and Wildlife Program, which call for initiating the actions set
forth in the Hungry Horse Implementation Plan. The Plan’s guidelines allowed managers to
proceed with native species restoration and enhancement (hatchery stocking) of offsite
fisheries in the Flathead Subbasin after Flathead Lake kokanee reintroductions were
unsuccessful.
        This proposal also partially satisfies a Flathead Subbasin management objective to
utilize hatchery production to stock offsite, closed-basin lakes in order to increase angler
opportunity and divert fishing pressure away from weak but recoverable wild native
populations already under limited or no-harvest fishing regulations.

             Review Comments
Monitoring for this project is preformed under Project Number 24019.

             Budget
             FY02                                  FY03                                    FY04
$106,672                            $109,872                                  $113,168
Category: High Priority             Category: High Priority                   Category: High Priority




Flathead Subbasin Summary                           78                                                  3/6/01
           New Projects


Project: 24012 – Riparian Habitat Preservation - Weaver Slough and McWinegar Slough


           Sponsor: Flathead Land Trust (FLT)
           Short Description:
Protect a range of natural resources compromised by rapid subdivision and development in
the Flathead River Subbasin. Acquisition of purchased easements on five properties will
extend private conservation of the Flathead River riparian corridor, permanently protecting
lowland/wetland habitats in two significant sloughs. Protecting these sloughs is a high
priority because of their value as resting and feeding sites for migratory waterfowl. A third
site, which would also be protected as a result of this project, has a large remnant black
cottonwood forest. It lies on a bend of the Flathead River that ongoing MFWP fisheries
studies show is a highly significant overwintering site for bull trout and westslope
cutthroat.


            Abbreviated Abstract
Acquire purchased easements from five landowners on tracts crucial to protecting the
mainstem Flathead River corridor. The sites will supplement other protected lands and
protect from subdivision a major portion of the remaining riparian habitat in the mainstem
Flathead River north of Flathead Lake. The tracts provide vital habitat for migratory
waterfowl, are part of the Pacific Flyway, and support a variety of bird, mammal, and
amphibian species that require riparian habitats. The project areas include two major
sloughs — Weaver Slough and McWinegar Slough — and a third tract on the Flathead
River called Foyís Bend. Foyís Bend includes substantial wetland and river frontage that
serves as overwintering habitat for native salmonids. The project preserves habitat types
that are otherwise decreasing in the Flathead Subbasin as a result of operations of Hungry
Horse Dam. Private land conservation is absolutely necessary to supplement public lands in
this ecosystem scenario because of the political liability of public land ownership in this
subbasin where the majority of land (more than 70 percent) is already in state and federal
ownership. Riparian lands have a disproportionately low representation in public holdings,
so preservation of private lands becomes essential to preserving the overall health of the
ecosystem. Projects demonstrate the strength of a partnership of farmland and habitat
protection to achieve multiple-benefit, landscape-scale preservation goals.




Flathead Subbasin Summary                    79                                      3/6/01
             Relationship to Other Projects

        Project ID                      Title                       Nature of Relationship
24018                      Secure and Restore Critical       Project #24018 focuses on
                           Fish and Wildlife Habitats        securing habitats through land
                                                             acquisition and conservation
                                                             easements in the southern part of
                                                             the subbasin, while this project
                                                             addresses habitats in the upper
                                                             basin.
20028                      Purchased Conservation            Comparable effort in our region
                           Easement from Plum Creek          to protect habitat on private lands
                           Timber Company (PCT)              in the Kootenai Basin
                           along Fisher River by
                           Montana Fish, Wildlife &
                           Parks (MT FWP)
                           Montana Ag Heritage               Sources of matching funds to
                           Program and NRCS                  complete the project
                           Farmland Protection
                           Program
                           Flathead Lakers Critical          Identifies area north of Flathead
                           Lands Workshop                    Lake as critical to lake protection
                                                             Research project in Upper
                                                             Flathead system to track
                                                             migratory patterns of native
                                                             salmonids - MT FWP Indicates
                                                             importance of Foyís Bend site
198905200                  Montana Wildlife Trust            Wildlife mitigation trust fund
                           MFWP Research project             Indicates importance of Weaver
                           (1987) - Effects of Water         and McWinegar Sloughs
                           Levels on Productivity of
                           Canada Geese in the
                           Northern Flathead Valley



             Relationship to existing goals, objectives and strategies
This project addresses the Flathead Subbasin management objective of protecting critical
wetland and riparian habitats through acquisition or conservation easements. Project areas
are high priority areas (Source: MFWP, Flathead Lakers, Flathead Land Trust, American
Bird Conservancy) for establishment of purchase/protection mechanisms. The project also
complements ongoing public and private conservation efforts to protect as much as
possible of the mainstem Flathead River riparian lands from subdivision and development.


             Review Comments
There appears to be an inconsistency in the ISRP's requests for M&E among project
sponsors. Standards do not appear to be the same from one project to the next. A
Monitoring and Evaluation plan was not requested by the ISRP for this project whereas


Flathead Subbasin Summary                           80                                             3/6/01
other similar projects were required to provide such information. This project presents a
unique situation where BPA dollars are being requested to maintain land for agricultural
use. According to language in the Farm Land Protection Program (USDA-NRCS), which
will be used for cost share to fund part of this project, participating landowners must
choose to keep their land in agriculture. BPA may not be the appropriate match source
under this language. If the BPA dollars were tied strictly to the riparian wetland portion of
this project, the funding category would have been identified as High Priority. If BPA
dollars were tied strictly to riparian/wetland portions, it would have ranked high priority.

              Budget
                 FY02                               FY03                       FY04
$1,080,000
Category: Recommended Action
Notes: If BPA dollars are tied
strictly to the riparian wetland
portion of this project; the funding
category would be High Priority.




Project: 24013 – Assessment of Operational Impacts of Hungry Horse Dam on Riparian
Wildlife habitats and their associated aquatic components


              Sponsor: Montana         Fish, Wildlife & Parks (MFWP)
              Short Description:
Enhance and protect native wildlife communities in the Flathead Subbasin through multi-
species assessments, design of habitat improvements, develop approaches to habitat
protection, mitigate variable river flows, and identify off-site mitigation potential.

              Abbreviated Abstract
Montana Fish, Wildlife & Parks is proposing a study to assess the operational impacts of
Hungry Horse Dam on riparian wildlife habitats and their associated aquatic components.
The results of this study would then be used to develop plans to mitigate wildlife habitat
impacts associated with power production. This study would build on efforts of the Hungry
Horse Fisheries Mitigation project (199101903) by extending these aquatic evaluations to
include operational impacts on adjacent riparian habitats and the terrestrial wildlife species
they support. By building on the fisheries work, we can develop an integrated model that
provides for the needs of power production and flood control, as well as fish and wildlife
populations and the successional processes that provide current and future habitat needs.
This is consistent with the Council’s revised approach of treating a given habitat as an
ecosystem that includes both fish and wildlife. Fish and aquatic invertebrate populations
are an integral part of the food chain supporting terrestrial wildlife populations. A plan to
sustain river processes that perpetuate seral plant communities that eventually develop into
mature riparian forests, will meet the overall vision of the Fish and Wildlife Program to




Flathead Subbasin Summary                           81                                3/6/01
protect and restore the natural ecological functions, habitats, and biological diversity of the
Columbia River Basin.

            Relationship to Other Projects
      Project ID                       Title                      Nature of Relationship
199101903                 Hungry Horse Fisheries      The project will continue the
                          Mitigation umbrella         landscape and systems approach
                                                      developed for the Fisheries
                                                      Program by monitoring and
                                                      assessing impacts on avian,
                                                      reptilian and amphibian species
                                                      associated with the riverine
                                                      habitats affected by dam
                                                      operations.
198905200                 Montana Wildlife Trust      Wildlife mitigation trust fund
1999RP11917               The Flathead River          This project will provide the
                          Instream Flow Investigation physical framework for assessing
                                                      changes in riverine habitat as a
                                                      function of dam operations

            Relationship to Existing Goals, Objectives and Strategies
Construction and inundation losses were documented for Hungry Horse Dam in 1984
(Casey et al. 1984). A wildlife mitigation plan was completed in 1985 (Bissell and Yde
1985) and was approved in the Council’s 1987 Fish and Wildlife Program. The 1988
Settlement Agreement between Bonneville Power Administration and the State of Montana
subsequently established the loss assessments for Libby and Hungry Horse (Casey et al.
1984, Yde and Olsen 1984) as the basis of the Montana Wildlife Mitigation Program. That
agreement further specified that the program should be consistent with the Council's
Columbia River Basin Fish and Wildlife Program, and that those measures in the Council's
program are given priority consideration.
        Casey and Wood (1986) evaluated operational impacts of Hungry Horse and Kerr
Dams on Canada geese in the Flathead River from Hungry Horse Dam to Flathead Lake.
Their study determined that Hungry Horse Dam had little effect on Canada geese. Bissell
and Bown (1987) did a parallel study of muskrat, beaver, otter, and mink on the section of
river influenced by Kerr Dam. They concluded that Kerr Dam effects dominate impacts to
these four species. However, neither study adequately addresses the question of ecosystem
function and fish or wildlife community issues that are a priority in the current Council
Program.
        Wildlife mitigation projects in the Flathead Basin of Montana have resulted in over
12,000 acres of wildlife habitat that have been enhanced or conserved since 1970. This
work has resulted in over 4,500 acres of mitigation credit for wildlife habitat losses
associated with Libby and Hungry Horse Dams (Wood 2000). We recently completed an
agreement with Plum Creek Timber Company to purchase a conservation easement on
140,250 acres of their land along the Thompson and Fisher Rivers. This project will easily
complete forest mitigation and most remaining riparian mitigation obligations. With
completion of most mitigation associated with construction of Hungry Horse Dam, it is an


Flathead Subbasin Summary                          82                                      3/6/01
opportune time to focus our attention on an operational impact assessment and mitigation
plan. In addition, it is important to work with the ongoing operational impact studies for
fisheries in the Flathead River to integrate with those efforts. Council’s current Fish and
Wildlife Program stated that operational and secondary losses have not been estimated or
addressed for terrestrial wildlife. However, the program includes a commitment to mitigate
for these losses.
        This project proposal is designed to address the following objective: complete an
operational impact assessment and develop plans to mitigate for any impacts that the
operations of Hungry Horse Dam may cause to the development and successional trends of
riparian wildlife habitats and their associated aquatic components, in cooperation with on-
going fisheries mitigation activities. With completion of most mitigation associated with
construction of Hungry Horse Dam, it is an opportune time to focus our attention on an
operational impact assessment and mitigation plan. In addition, it is important to work with
the ongoing operational impact studies for fisheries in the Flathead River to integrate with
those efforts. Council’s current Fish and Wildlife Program stated that operational and
secondary losses have not been estimated or addressed for terrestrial wildlife. However, the
program includes a commitment to mitigate for these losses.
           Review Comments
Operational loss assessments are emphasized as a priority in the subbasin summary. A
more detailed description of proposed activities is needed to rank this project in a higher
category. From the proposal, this project is for assessment and monitoring to develop the
methods to mitigate. This makes it difficult to apply these criteria to the project.

           Budget
             FY02                               FY03                           FY04
$188,949                          $191,249                        $118,641
Category: Recommended Action      Category: Recommended Action    Category: Recommended Action




Project: 24018 – Secure and Restore Critical Fish and Wildlife Habitats


           Sponsor: Confederated Salish and Kootenai Tribes (CSKT)
           Short Description:
Utilize land acquisition and habitat restoration to protect and enhance habitats critical to
fish and wildlife. Reduce human-wildlife conflicts on acquired and restored lands to
increase their value for wildlife.

           Abbreviated Abstract
When Hungry Horse Reservoir filled, 23,750 acres of low elevation forest, wetland, and
riparian habitats were inundated, including seasonal habitat for a wide variety of avifauna,
spring and fall grizzly bear habitat, and important big game range and calving areas.
Similarly, the construction and operation of Libby Dam resulted in the direct loss of 28,850


Flathead Subbasin Summary                      83                                    3/6/01
acres of wildlife habitat. To replace these lost fishing and hunting resources and plant
harvesting and spiritual sites, the Salish and Kootenai Tribes have been forced to rely more
heavily on Reservation lands, which in turn have been degraded from over one-hundred
years of private and federal land management and development activities. Rapid residential
and commercial growth now threatens the best remaining habitats.
    Low elevation spring and fall grizzly bear habitat on the Reservation is decreasing,
while the level of disturbance and the number of conflicts with private landowners are
increasing. Similarly, because of the limited amount of winter range and chronic conflicts
with surrounding ranchers, Tribal biologists now manage elk within the Ferry Basin Elk
Conservation Area well below what the summer range could support. Rapid growth and
development near or adjacent to lakes and streams has resulted in the loss or degradation of
significant riparian and wetland habitats, which in turn has resulted in much lower fish and
wildlife numbers than could otherwise be achieved.
    This project proposal will address these problems by 1) securing habitats through land
acquisition and conservation easements; (2) enhancing existing and newly acquired
habitats to maximize their value to fish and wildlife; (3) creating a wildlife-conflicts
specialist position to resolve wildlife conflicts with surrounding landowners and implement
proactive projects to resolve conflicts; and (4) utilizing a balanced system-wide, watershed
approach to reverse the downward trends in native species and protect healthy populations.
Target species include grizzly bear, elk, all native riparian species, cutthroat trout and bull
trout.

           Relationship to Other Projects
      Project ID                      Title                   Nature of Relationship
9101903                  Flathead Watershed             Implements mitigation plan
                         Restoration and Monitoring
9101901                  Flathead Lake Monitoring and   Formerly a stand-alone project, now
                         Habitat Enhancement            part of this project. Purpose is habitat
                                                        restoration and monitoring.
9608701                  Focus Watershed Coordination   Formerly a stand-alone project, now
                         - Flathead River Watershed     part of this project. Directly assists
                                                        the accomplishment of project
                                                        objectives by coordinating with
                                                        agencies and landowners to
                                                        implement mitigation measures.
9520500                  Flathead River Instream Flow   Instream habitat restoration
                         Project
0                        Hungry Horse Dam Wildlife      Co-sponsor of Dayton Creek
                         Mitigation                     restoration project and other possible
                                                        conservation easements (Montana
                                                        Wildlife Trust Fund).
0                        Kerr Project Habitat           Potential for partnering/cost share on
                         Restoration and Acquisition    projects and complementary projects
0                        Jocko River Wetland/Riparian   Potential for partnering/cost share on
                         Habitat and Bull Trout         projects and complementary projects
                         Restoration Plan
                         Implementation
0                        CSKT land acquisitions         Complements restoration efforts
0                        Misc. CSKT Habitat             Potential for partnering/cost share on



Flathead Subbasin Summary                       84                                                 3/6/01
     Project ID                       Title                       Nature of Relationship
                         Improvement and Restoration      projects and complementary projects
                         Projects
0                        Kicking Horse Habitat            Restore low elevation riparian and
                         Restoration Project              wetland habitats used by grizzlies on
                                                          a prior Tribal Range Unit.
0                        Poison-oak Riparian              Restore low-elevation riparian and
                         Restoration Project              aspen seep habitat in area used
                                                          extensively by grizzly bears.


           Relationship to Existing Goals, Objectives and Strategies
This project address the following goal of the 1994 Fish and Wildlife Program (FWP): the
rebuilding to sustainable levels of weak, but recoverable, native populations injured by the
hydropower system. Specific objectives in the FWP addressed by this project include:
7.7A, 7.7|B, 10.2A.2, 10.2B, 10.2B.1, 10.2C.4, 10.3A.2, 10.3A.4, 10.3A.10, 10.3A.11,
10.3A.13.
    The 1993 USFWS Grizzly Bear Recovery Plan specifically identifies the importance of
maintaining grizzly bears in the Mission Mountains. In outlining criteria for recovery of
grizzly bears in the Northern Continental Divide Ecosystem, the plan states: ―Furthermore,
recovery cannot be achieved without occupancy in the Mission Mountains portion of this
ecosystem.‖ Paramount to maintaining occupancy of grizzly bears is the protection and
enhancement of remaining low elevation habitat. In a letter dated May 29, 1998 the U.S.
Fish and Wildlife Service Grizzly Bear Recovery Coordinator stated, ―I believe that
without the maintenance of large blocks of undeveloped land along the west slope of the
Missions, the probability of maintaining a grizzly bear population in the Mission
Mountains is very low.‖
    Maintaining grizzly bear populations on the Flathead Indian Reservation is a major
goal of the CSKT as well. The CSKT developed a Grizzly Bear Management Plan in 1981.
That plan outlines management direction and priorities to maintain grizzly bear
populations, and acquisition and conservation easements were identified as a priority. The
plan also acknowledges resolving human/bear conflicts as an important part of protecting
grizzly bear populations.
        For fish habitat, this project works to achieve the goals and objectives of the FWP
by implementing measures that mitigate the loss of fish habitat resulting from construction
of Hungry Horse Dam. These measures have included direct supplementation and habitat
restoration. Implementation of the project will be conducted in close cooperation with
Project No. 9101903, which represents a necessary collaborative effort between the State
and the Tribes, who share jurisdiction and management in the basin.
        The Focus Watershed component of this project complements other projects such
as the Excessive Drawdown Mitigation Program (project 940100), Hungry Horse
Mitigation/Habitat Improvements (9101903), Hungry Horse Fisheries Mitigation
(9101901), Hungry Horse Mitigation (9101904) and its sister project in the Kootenai River
system (9608702). It is supported by Montana Fish Wildlife and Parks; the Flathead Basin
Commission; Lake, Lincoln, Sanders, and Flathead County Conservation Districts; the
Natural Resource Conservation Service; Citizens for a Scenic Lake County; and Flathead
Lake Biological Station. Activities are being coordinated with these agencies and groups to



Flathead Subbasin Summary                         85                                              3/6/01
implement plans and projects in the future. All of these activities further the Tribal and
State goals of habitat restoration being conducted from a coordinated, watershed
perspective.
        This project also directly address the following objectives of subbasin management
agencies: (1) Acquire and/or protect key habitat parcels (endangered, threatened, and
sensitive species habitats) through purchase, conservation easements, or conservation
agreements to assist in maintenance of viable populations. (2) Protect, restore, and enhance
riparian/wetland habitats. Protect critical areas through acquisition or conservation
easements. Work through the Focus Watershed Coordination project to identify site-
specific wetland/riparian restoration projects and to coordinate with landowners, agencies,
and other funding sources. (3) Deal with ongoing recreation-fisheries-water quality
conflicts on a daily basis, and educate the public to reduce these conflicts. (4) Significantly
reduce the level of sedimentation in impacted spawning areas by restoring normative
surface-water runoff patterns in upland areas using best management practices and habitat
improvement measures and by restoring natural stream channel function and form using
soft methods. (5) Maintain temperatures within the tolerance range of native fish species by
improving riparian and in-stream habitat using stream channel and riparian habitat
restoration methods as described by Rosgen 1995. (6) Deal with ongoing human-wildlife
conflicts on a daily basis, and educate the public to reduce human-wildlife conflicts.


             Review Comments
There is an agreement between BPA and MFWP regarding wildlife credits for the state of
Montana. The CSKT is not a signatory to that agreement and believe that most of the credits to
date have occurred in areas that are not accessible to tribal members. An adequate M&E plan is
presented in the proposal, but a direct link to objectives is not clear.


             Budget
             FY02                                  FY03                          FY04
$4,918,444                          $4,538,826                      $4,538,826
Category: High Priority             Category: High Priority         Category: High Priority




Project: 24019 – Research, Monitor, and Restore Native Species


             Sponsor: Confederated Salish and Kootenai Tribes   (CSKT)
             Short Description:
Implement and monitor fisheries improvement activities for native species and conduct a
feasibility study on the reintroduction of sharp-tailed grouse. Research factors limiting the
successful application of mitigation and restoration measures.
             Abbreviated Abstract
This project seeks to determine how habitat changes, species shifts, and the consequent
dominance of new species—factors that have the potential to limit the success of


Flathead Subbasin Summary                          86                                    3/6/01
mitigation measures—have affected native species. It also seeks to determine status of a
locally extirpated species—sharp-tailed grouse— and whether reintroduction is feasible.
The project has two main components.
        The fisheries component is a continuation of portions of BPA project number
9101901. That project, initiated in 1992, has been documenting trends in westslope
cutthroat trout and bull trout populations and changes in the populations of several other
major species through standardized gillnetting surveys; conducting creel surveys that have
defined the baseline condition of the Flathead Lake fishery in 1992-1993 and 1998-99;
examining the competitive interactions with lake trout and Mysis relicta, and the possible
absence of such species as white sturgeon; and conducting basic research into food web
interactions and factors controlling lake trout abundance (the predatory influence of lake
trout on native species is high). This work includes cooperation with state management
agencies and two universities. We have learned that this basic research is necessary to
successfully mitigate losses of adfluvial trout in Flathead Lake.
        The wildlife component is a three-year feasibility study to determine the status of
existing habitat for Columbian sharp-tailed grouse in northwestern Montana and the
potential for population augmentation and/or reintroduction in the most favorable areas.
The suitability of habitat will be evaluated by a landscape-level evaluation of available
potential habitat using Geographical Information System (GIS) analysis. This methodology
will provide a foundation for a more detailed analysis of features important to nesting and
over-wintering sharp-tailed grouse. The detailed analysis will entail ground-truthing of
potential habitat areas to determine sites that actually contain suitable habitat for nesting
and over-wintering grouse and identify the sites that might be able to support populations
of grouse. The project will also examine the potential for population augmentation or
reintroduction at high priority sites. An additional objective of this component will be to
determine the methods necessary to achieve the long-term goal of restoration of Columbian
sharp-tailed grouse as a viable population in northwestern Montana.


           Relationship to Other Projects
      Project ID                      Title                   Nature of Relationship
9101903                  Flathead Watershed             Implements mitigation plan
                         Restoration and Monitoring
9502500                  Flathead River Instream Flow   Instream habitat restoration
                         Project

9608701                  Focus Watershed Coordination   Directly assists the accomplishment
                         - Flathead River Watershed     of project objectives by coordinating
                                                        with agencies and landowners to
                                                        implement mitigation measures.
                         Hungry Horse Dam Wildlife      Co-sponsor of Dayton Creek
                         Mitigation                     restoration project and other possible
                                                        conservation easements with
                                                        Montana Wildlife Trust Fund
9101904                  Non-native fish                Native/non-native species interaction
                         removal/hatchery production    research; offsite mitigation for
                                                        Flathead Lake.




Flathead Subbasin Summary                       87                                               3/6/01
             Relationship to Existing Goals, Objectives and Strategies
The goal of the 1994 Fish and Wildlife Program addressed by this project is the rebuilding
to sustainable levels of weak, but recoverable, native populations injured by the
hydropower system. Specific objectives in the FWP include: 7.7A, 7.7|B, 10.2A.2, 10.2B,
10.2B.1, 10.2C.4, 10.3A.2, 10.3A.4, 10.3A.10, 10.3A.11, 10.3A.13.
        The fisheries component of this project works to achieve the goals and objectives of
the FWP by monitoring measures that mitigate the loss of habitat resulting from
construction of Hungry Horse Dam. Mitigation measures being monitored have included
direct supplementation and habitat restoration. Additionally, this project monitors tributary
restoration projects directly and on a larger scale in Flathead Lake, so that the feedback
loop remains intact. Monitoring is conducted in close cooperation with Project No.
9101903, which represents a necessary collaborative effort between the State and the
Tribes, who share jurisdiction and management in the basin.
        The fisheries component directly addresses the high-priority Flathead Subbasin
Summary objective to reduce negative nonnative species interactions in Flathead Lake.
        The wildlife component is consistent with the Northwest Power Planning Council’s
1994 Fish and Wildlife Plan system-wide goal of a healthy Columbia River Basin. It is
appropriate under language in Section 11, complies with Section 11.2D, and is consistent
with Section 11.2E. The Columbian sharp-tailed grouse is listed as a target species of high
priority in the Upper Columbia Sub basin in Section 11.2E. The project directly addresses
the subbasin summary management objective to develop a reintroduction plan for
Columbian sharp-tailed grouse in the Flathead Basin by working with private, Tribal, State,
and federal landowners to identify opportunities to restore habitat and populations. The
well-being and continued existence of Columbian sharp-tailed grouse and its habitat has
been the focus of efforts by Montana Fish, Wildlife and Parks for the past fifteen years,
with population augmentation efforts initiated in Lincoln County. The species has also
been the subject of surveys conducted by the Confederated Salish and Kootenai Tribes. The
Tribes cultural resource staff also strongly support reintroduction. The National Bison
Range has expressed a strong interest in the re-establishment of Columbian sharp-tailed
grouse on its lands as has the U. S. Forest Service.


             Review Comments
Since the fisheries objectives are unclear it is difficult to determine if the monitoring
proposed here is addressing those objectives.

             Budget
             FY02                                  FY03                               FY04
$131,400                            $144,500                             $139,500
Category: High Priority             Category: High Priority              Category: High Priority




Flathead Subbasin Summary                           88                                        3/6/01
           Research, Monitoring and Evaluation Activities
Existing monitoring and evaluation activities for fish include collecting micro- and macro-
habitat parameters (i.e. depth, velocity, substrate, habitat type etc.) for use in developing
weighted useable area curves for size-classes of bull trout and westslope cutthroat trout.
This information will be used to develop habitat suitability use curves required by the
Instream Flow Incremental Methodology (IFIM) Project (BPA #9502500) on the Flathead
River. MFWP will monitor river temperatures at six locations in the Flathead River
system; quantify differences in macrozoobenthos diversity and abundance and pre- and
post-selective withdrawal; and quantify and compare whitefish growth rates pre and post.
This information will serve to monitor the effects of selective withdrawal at Hungry Horse
Dam on Flathead River ecosystem. To assess abundance, distribution, and food habits of
predator fish species (lake trout, northern pike) in the mainstem, north, and middle forks of
the Flathead River, MFWP will perform creel surveys throughout the Flathead River
system; obtain growth information and analyze stomach contents from harvested northern
pike and lake trout; and tag and release fish for abundance and distribution analyses. To
assess distribution and movements of juvenile, sub-adult, and adult bull trout and
westslope cutthroat trout in the mainstem, north, and middle forks of the Flathead River,
MFWP will use radio-telemetry to collect data on bull trout distribution, movement, and
habitat use through weekly ground, boat, and aerial surveys. To assess distribution and
movements of westslope cutthroat trout, rainbow trout, and WCT x RBT hybrids in the
mainstem, North, and Middle forks of the Flathead River, MFWP will collect data on
westslope cutthroat trout distribution, movement, and habitat use through weekly ground,
boat, and aerial surveys.
        To monitor watershed-level fish and habitat parameters MFWP will annually
monitor spawning (incubation and habitat quality by McNeil method of streambed coring
in 33 tributaries to assess juvenile bull trout rearing habitat quality and by substrate scoring
in 21 tributaries); conduct annual migratory cutthroat and bull trout redd counts in 45 index
tributary reaches to monitor adult runs; conduct annual cutthroat and bull trout juvenile
estimates in 31 tributaries to monitor recruitment; conduct river population estimates in
mainstem and the three forks of Flathead River; conduct annual gill net series on Flathead
Lake and Hungry Horse Reservoir; and collect disease samples from wild fish populations.
        MFWP will evaluate past mitigation projects on Taylor's Spring Creek, Hay Creek,
Dayton Creek and monitor fish growth, species composition, and angler use at past lake
rehabilitations on Lion, Rogers, Bootjack, Murray, and Dollar lakes plus other offsite fish-
plant waters. A specific monitoring strategy, including pre- and post-treatment sampling, is
designed for each restoration project. These are combined with watershed-level spawning
substrate and redd counts, electrofishing, and gillnet monitoring series to assess direct and
indirect effects of the program.
        MFWP will assess the timing and magnitude of discharge releases (e.g. ramping
rates and flow regimes) from Hungry Horse Dam as related to the distribution, habitat use,
and movements of juvenile and adult bull trout and westslope cutthroat trout. MFWP will
quantify impacts of flow releases from Hungry Horse Dam on the macroinvertebrate
community structure and temporal frequency dynamics of trophically important benthic
species in the Flathead River downstream of Hungry Horse Dam. MFWP will also conduct




Flathead Subbasin Summary                     89                                        3/6/01
research on an as-needed basis as specified in the USFWS Biological Opinion on bull trout
in the upper Flathead River system.
CSKT will monitor: native species abundance in Flathead Lake using spring gillnetting, the
biology of lake trout in Flathead Lake using fall gillnetting, the success of offsite fish
plants through creel surveys and fish sampling, and exploitation rates of sport fish in
Flathead Lake using a year-long creel survey. The Watershed Focus Coordinator's
effectiveness will be monitored by tracking the number of individuals in the subwatershed
participating in restoration activities. In addition, CSKT Fisheries and Water Management
programs will monitor: native fish populations on a 10-year cycle to evaluate long-term
viability based on the BayVam or similar model by measuring abundance, available
habitat, and year-class distribution; substrate condition by McNeil coring or substrate
embeddedness in all streams on a 15-year cycle; channel complexity in all streams on a 15-
year cycle; and streams by maintaining and intermittently reporting results for the
Reservation-wide Stream Assessment and Reference-reach Assessment Monitoring
Program. For timber sales, the Tribes will monitor BMP implementation and road
abandonment and cumulative effects. They will also conduct sediment source surveys,
stream and wetlands inventories, and forest-wide stream-reach assessment surveys for 16
reaches.
        In 1999, Montana initiated a modified Instream Flow Incremental Methodology
(IFIM) project on the Flathead River to refine the river component of HRMOD. The
project has been approved for two years of funding and the final year, FY2000, is pending
NWPPC approval. The IFIM research will calibrate simulations of hydraulic conditions
(stage/discharge and velocities etc.) and fish habitat from Hungry Horse Dam to Flathead
Lake at various discharges from Hungry Horse Dam. An optimization program is
scheduled for development to allow managers to assess tradeoffs between the requirements
of reservoir and riverine biota, when conflicts occur between reservoir operation and river
flow limits as per the MFWP. MFWP and CSKT monitor the effects of dam operation in
Hungry Horse Reservoir and the Flathead River and its tributaries.
        Factors controlling Mysis abundance in Flathead Lake will be researched by CSKT
through biweekly Mysis sampling with associated limnological parameters.
        The U.S. Forest Service conducts periodic physical and biological stream surveys
and wildlife inventories on subbasin federal lands. Water quality monitoring is ongoing by
a number of agencies.
        With respect to wildlife, a nongame monitoring program by MFWP will evaluate
the effects of habitat enhancements at Hungry Horse on breeding-bird communities to
determine if enhancement prescriptions for big game species effectively restore habitat for
bird species as well. A final summary report of this eight-year effort will be prepared by
June 2001. The results will be used to review and develop new habitat enhancement
proposals and methods for measuring wildlife benefits. Big game monitoring will evaluate
the effectiveness of big game habitat enhancements along Hungry Horse Reservoir. A final
summary report of this 13-year effort will be prepared by June 2001. The results will be
used to review and develop new habitat enhancement proposals and methods for measuring
wildlife benefits. MFWP conducts population monitoring on big game, furbearer, and
nongame populations in the subbasin annually through a variety of surveys and inventories.
It conducts annual surveys of elk, mule deer, white-tailed deer, moose, mountain goats, and


Flathead Subbasin Summary                   90                                     3/6/01
grizzly bears. The agency also conducts breeding bird surveys on each of their wildlife
management areas as well as furbearer track surveys during winter.
         The Montana Bald Eagle Working Group and the Montana Loon Society coordinate
annual bald eagle and common loon occupancy and productivity surveys. The National
Audubon Society sponsors annual Christmas bird counts. The U.S. Fish and Wildlife
Service coordinates annual breeding bird surveys in the Flathead Subbasin as part of the
national surveys. There are also MAPS (Monitoring Avian Production and Survivorship)
stations conducted each year, an effort coordinated by the Point Reyes Bird Observatory in
California.
         As part of its management program, the CSKT Wildlife Management Program
monitors wildlife populations on the Flathead Indian Reservation and in adjacent habitats.
Big game, waterfowl, upland gamebirds, endangered, threatened and sensitive species,
nongame species, furbearers, amphibians, and reptiles are routinely monitored. The Tribes
track the recovery of endangered and threatened species by continuing to monitor
populations in coordination with other State and federal agencies. They also monitor
activities designed to eliminate or mitigate the impacts of activities such as forest
management, range management, construction, and a variety of other developments.
         Wildlife research includes a long-term black bear study designed to improve
harvest criteria used for management by assessing the vital rates (reproduction and
mortality) of a typical black bear population in Swan River Valley. The project is also
documenting local population size, trend, and sustainable harvest level estimates.
Simultaneously, the project will develop estimates of black bear population size in typical
hunting areas throughout western and central Montana to estimate current harvest rates.
Long-term monitoring and associated research on the Flathead Indian Reservation includes
work on bald eagles, small mammal population dynamics and their impacts upon other
species, grizzly bears, amphibians, and forest carnivores.

New proposals include the following research, monitoring and evaluation activities:

    Project 24012 will conduct at least annual monitoring of the project site (visits to five
    landowners) to assure adherence to easement terms.

    Project 24013 will monitor and assess populations of birds and herpitiles associated
    with riparian habitats by conducting amphibian and reptile surveys, establishing avian
    point count locations, conducting avian point counts

    Project 24018 will:
       1. Monitor the terms of acquired conservation easements. A schedule and system
           will be established to monitor the conditions of conservation easements. Land
           technicians will work with landowners to assure compliance.
       2. Monitor the implementation and success of management plans and restoration
           efforts. Periodic measures will be obtained at five-to-ten-year intervals to
           compare with baseline information as described in Task a. Aerial photographs
           will be obtained to monitor major shifts in plant communities. The coverage of
           noxious weeds will be estimated and monitored on all properties. Within


Flathead Subbasin Summary                   91                                      3/6/01
         grasslands the species composition of the plant community, a measure of winter
         range productivity, and a measure of nesting cover using Visual Obscurity
         Readings (Martin et al. 1997) will be monitored. For riparian and wetland
         habitats, health assessments (RWRP 2000) will be conducted for a baseline to
         be compared with future assessments collected on a five-to-ten-year interval.
      3. Monitor the success of conflict projects. The conflict specialist will work with
         cooperating residents, landowners and businesses to monitor the success of
         conflict projects. Success will be measured by elimination of, or significant
         reductions in, human-wildlife conflicts at the site.
      1. Monitor the physical and biological responses to implemented restoration
         measures.
      2. Develop a predictive model of shoreline erosion potential in Flathead Lake.

    Project: 24019 will:
        Monitor native species abundance through a trend analysis , conduct an annual
           creel survey, monitor lake trout biology through a trend analysis, and monitor
           off-site stocking through returns and survival analysis
        Research Mysis dynamics and interactions


    Project 199101903 will:
       Collect micro and macro habitat parameters (i.e. depth, velocity, substrate,
          habitat type etc.) for use in developing weighted useable area curves for size-
          classes of bull trout and westslope cutthroat trout.
       Monitor river temperatures at 6 locations in Flathead River system
       Quantify differences in macrozoobenthos diversity and abundance pre- and
          post-selective withdrawal.
       Quantify and compare whitefish and trout growth rates pre- and post.
       Periodically perform seasonal creel surveys throughout the Flathead River and
          upper Flathead Lake.
       Obtain growth information and analyze stomach contents from harvested
          northern pike and lake trout.
       Tag and release fish for abundance and distribution analyses.
       Estimate catch rates of bull trout in the Flathead River and upper Flathead Lake.
       Collect data on bull trout distribution, movement and habitat use through
          weekly ground, boat and aerial surveys.
       Collect data on distribution, movement and habitat use by the study fish through
          weekly ground, boat and aerial surveys.
       Identify and prioritize source hybridization streams.
       Annually monitor spawning, incubation and habitat quality by McNeil method
          of streambed coring in 33 tributaries to assess juvenile bull trout rearing habitat
          quality, and by substrate scoring in 21 tributaries.
       Conduct annual migratory cutthroat and bull trout redd counts in 45 index
          tributary reaches to monitor adult runs.



Flathead Subbasin Summary                   92                                      3/6/01
          Conduct annual cutthroat and bull trout juvenile estimates in 31 tributaries to
           monitor recruitment.
          Conduct river population estimates in main stem and forks of Flathead River.
          Conduct annual gill net series on Flathead Lake and Hungry Horse Reservoir.
          Collect disease samples from wild fish populations.
          Assess changes in fish behavior and habitat use under various ramping rates
           using radio-telemetry.
          Quantify differences in macrozoobenthos diversity and abundance under
           various operating strategies.
          Monitor habitat conditions and fish populations at individual mitigation sites
           including Emery Creek, Taylor Spring, and Hay, Robertson, Griffin and Dayton
           Creeks.
          Monitor fish growth, species composition, and angler use at past lake
           rehabilitations on Whale, Tom Tom, Lion, Rogers, Bootjack, Murray, & Dollar
           lakes.
          Initiate a basin-wide water chemistry analysis of the South Fork Flathead River
           to assess the feasibility of using radio-isotope markers and nuclear DNA
           techniques to identify bull trout and cutthroat trout natal streams.



           Needed Future Actions
For species adversely affected by hydropower operations, there is a need to conclusively
document population trends for target and high priority species along with any other
species that show declining populations and take actions for species recovery.
        There is a need to fund a future effort in the subbasin to prioritize potential
easements based on wildlife values so we can systematically save the best remaining lands.
There is a need to have ongoing funding for conservation easements as a way of making
conservation dollars go farther than through acquisition and to keep land in private
ownership, which is extremely important in the context of the local political environment.
        Funding needs to be increased for laboratory research on better ichthyotoxins
designed to remove exotic aquatic species, especially in running-water environments.
Toxins need to be undetectable by target organisms so those organisms cannot avoid them.
The toxins should also be irreversible so that the organisms cannot recover by entering a
spring source or turbulent, oxygenated waters. Finally, the toxin should be easily detoxified
or have a short period of toxicity before breaking down into an inert state. In Flathead
Lake, there is a need to fund research into the development of a species-specific toxin for
mysis.
        System hydrology models need to be expanded to allow weekly time-step
simulation of water routing within and between federal dam projects (ACOE, BPA and
BoR). Monthly models need to be refined to achieve weekly time resolution, to incorporate
estimates of unregulated local inflows, and to allow user control of inflow data from
unregulated sources so that historic flow records or calculated inflow files can be input to
model simulations.




Flathead Subbasin Summary                    93                                     3/6/01
        There is a need to establish a stepwise approach for monitoring BPA mitigation
projects: first monitoring site-specific results at individual mitigation projects, then
periodically measuring whole system responses. There is a need to schedule short-term and
long-term monitoring of individual mitigation projects.
        There is a need to increase patrols by enforcement officials to protect bull trout
during their spawning migration. Bull trout are vulnerable to illegal harvest while they are
in headwater tributaries. Enforcement patrols need to be increased in known spawning
habitats.


           Actions by Others
Agencies need to conclusively document population trends and develop coordinated
recovery plans for high-priority management species and other species that show declining
populations.
         County commissions and tribal governments should work together to insure that
comprehensive land use planning occurs in the subbasin to prevent development in
floodplains, wildlife habitats, wetlands, riparian areas, and hazard areas. Zoning regulations
that disallow any new development in floodplains need to be implemented. There is also a
need to enact and enforce regulations that deny new permits for septic systems and wells
within the 100-year floodplain boundary. Governmental jurisdictions should also develop
and enforce local regulations designed to minimize potentials for future wildlife-human
conflicts.
     Local, state, and federal governments and non-governmental institutions and
corporations need to create incentives to move existing human developments out of
floodplains. For example, the state and federal government could provide funds for the
relocation of homes and outbuildings currently located within the floodplain through
programs like ―Project Impact‖, a federal disaster prevention initiative. After providing
assistance to relocate, state and federal disaster relief should be terminated for those who
choose to live in the floodplain. Insurance companies should deny flood insurance for
homes and outbuildings located in the floodplain. Agencies should purchase lands or
obtain management rights for floodplain areas protected by dykes or levees and reconnect
those areas to the floodplain (cooperative cost-shares with ACOE, irrigation districts,
USFWS recovery funding for ESA-listed species and potential BPA cost-shares).
Agricultural uses of floodplains could continue where agriculture does not impact wetlands
or riparian buffer areas. The federal government could regulate agricultural revenues to
offset ―bust‖ years when crops are lost due to flood.
     There is a need to develop international, interstate, and interagency cooperative
initiatives to prevent the introduction and spread of aquatic nuisance species. Public
outreach and education should occur through schools, lake-homeowner associations,
sporting groups, and agencies. These activities could be sponsored through irrigation
districts, state and provincial departments of natural resources and conservation, fish and
wildlife, environmental quality, transportation, and agriculture, the U. S. Forest Service and
the Environmental Protection Agency.
     There is a need to foster greater grassroots support to implement conservation measures
on private lands. Agencies could help private groups acquire grants and assist with project



Flathead Subbasin Summary                    94                                      3/6/01
design and implementation and facilitate cost-share arrangements. Strategies need to be
developed to educate private landowners on how to coexist with wildlife and preserve or
enhance habitat. Agencies need to develop and/or implement other land and resource-
management plans that include the use of conservation easements or land acquisition that
will result in improved water quality and fish and wildlife habitat. Training for farmers and
ranchers that teaches ecologically compatible agricultural practices could be provided.
Workshops could demonstrate methods of water conservation and rest/rotation grazing
adjacent to streams and wetlands to eliminate or reduce livestock damages. They could
show agricultural producers how to establish natural fence rows and teach techniques for
protecting and restoring riparian areas and wetlands.
         There is a need to develop a basin-wide plan and regulations for off-stream water
development. Water diversions could be replaced with solar powered wells on higher
elevation water sources. Water conservation at irrigation projects could be improved
through moisture sampling in fields. Remote sensing could be used to assure fields are not
over watered.
         There is a need to develop cost-share to chemically rehabilitate Lake Mary Ronan
to remove illegally introduced yellow perch and reestablish a popular salmonid fishery. A
late-fall treatment, just before ice formation, would provide the greatest potential for a
complete kill.
         The Montana Department of Transportation and county road programs should seek
alternative alignments and other long-term roadway solutions to address channel
confinement. The state should identify and mitigate cumulative impacts associated with
new highway construction, improvement, or expansion projects.
         BPA-funded actions need to be more closely coordinated with the actions of other
agencies and organizations that are directed at benefiting fish and wildlife and their
habitats. There are, for example, an array of on-going conservation activities occurring in
the basin by agencies and groups like the conservation districts, the Natural Resource
Conservation Service, the US Fish and Wildlife Service, the Flathead Basin Commission,
and Flathead Lakers. The Confederated Salish and Kootenai Tribes have two major
wetland and riparian acquisition/restoration initiatives underway that are funded by Kerr
Mitigation and ARCO settlement dollars. Whenever it is appropriate, coordination and
cooperation between the various groups and jurisdictions involved in conservation could
enhance projects and help conservation dollars stretch farther.




Flathead Subbasin Summary                    95                                      3/6/01
          Table 1. Flathead River Subbasin Summary FY 2002 - 2004 BPA Funding Proposal Matrix




                                                                          199101903

                                                                                        199101904

                                                                                        24012

                                                                                                                    24013

                                                                                                                                  24014

                                                                                                                                                24018

                                                                                                                                                              24019
Project Proposal ID




                                                                                        5
                                                                          Urgent/High

                                                                                        Urgent/High

                                                                                                      Urgent/High


                                                                                                                    Urgent/High

                                                                                                                                  Urgent/High

                                                                                                                                                Urgent/High

                                                                                                                                                              Urgent/High
                                                                          Priority

                                                                                        Priority

                                                                                                      Priority


                                                                                                                    Priority

                                                                                                                                  Priority

                                                                                                                                                Priority

                                                                                                                                                              Priority
Provincial Team Funding Recommendation




These project titles are referenced by ID above:
199101901- Hungry Horse Mitigation - MFWP
199101904- Stocking of Offsite Waters for Hungry Horse Mitigation – Creston National Fish Hatchery - USFWS
24012 – Riparian Habitat Preservation – Weaver Slough & McWinegar Slough - FLT
24013 – Assessment of Operational Impacts of Hungry Horse Dam on Riparian Wildlife Habitats and Their Associated Aquatic
Components - MFWP
24014 - Assessment of Operational Impacts of Libby Dam on Riparian Wildlife Habitats and Their Associated Aquatic
Components - MFWP
24018 – Secure and Restore Critical Fish and Wildlife Habitat – CSKT
24019 – Research, Monitor and Restore Native Species - CSKT

         Note: + = potential or anticipated effect on subbasin objectives and strategies.




         Flathead Subbasin Summary                              96                                                                                                    3/6/01
                            Appendix A



           HATCHERY AND GENETIC
             MANAGEMENT PLAN
                Creston National Fish Hatchery




Flathead Subbasin Summary       97               3/6/01
  HATCHERY AND GENETIC MANAGEMENT PLAN
          RESIDENT FISH VERSION
                (HGMP-RF)




                      Hatchery Program: Stocking of Offsite Waters
                               Hatchery Program:
                      for Hungry Horse Mitigation-Creston NFH


                      Species or Hatchery Population/Strain:bull
                                     Species or
                      trout, Westslope cutthroat trout, rainbow trout
                                 Hatchery Stock:

                      Agency/Operator: USFWS-Creston National
                               Agency/Operator:
                      Fish Hatchery

                            Watershed and Flathead
                      Watershed and Region: Region: Subbasin,
                      Mountain-Columbia Province

                      Date Submitted: 9/29/00
                               Date Submitted:

                       Date Last Updated:
                               Date Last Updated:




Flathead Subbasin Summary                98                             3/6/01
SECTION 1. GENERAL PROGRAM DESCRIPTION

1.1)   Name of hatchery or program.
       Stocking of offsite waters for Hungry Horse fisheries mitigation – Creston National Fish
       Hatchery

1.2) Species and population (or strain) under propagation, ESA/population
status.
        Westslope cutthroat trout, Oncorhynchus clarki lewisi
        Rainbow trout, Oncorhynchus mykiss
        Bull trout, Salvelinus confluentus - threatened species

1.3)   Responsible organization and individuals

       Name (and title): Donald A. Edsall, Hatchery Manager
       Agency or Tribe: US Fish and Wildlife Service
       Address: 780 Creston Hatchery Road, Kalispell, MT 59901
       Telephone: (406)-758-6870
       Fax: (406)-758-6877
       Email: donald_edsall@fws.gov

       Other agencies, Tribes, co-operators, or organizations involved, including
       contractors, and extent of involvement in the program:
       Montana Department of Fish, Wildlife, and Parks (MDFWP) and the Confederated Salish
       and Kootenai Tribes (CSKT) manage the waters stocked under this program.

1.4)   Funding source, staffing level, and annual hatchery program operational costs.
       This program funded by Bonneville Power Administration.
       The annual budget for 2001 is $173,292, and includes 1.95 FTE’s

1.5)   Location(s) of hatchery and associated facilities.
       The Creston NFH is located on Mill Creek, a tributary of the Flathead River located
       several miles above Flathead Lake in northwest Montana.
       Latitude 48d-12min-30sec North, Longitude 114d.-7min-30sec West

1.6)   Type of program(s).
       Stocking portion of program is isolated harvest of Westslope cutthroat trout and rainbow
       trout from waters lacking natural reproduction or connection to natural populations.
       Culture of bull trout is for development of rearing techniques and provision of eggs for
       research purposes.




Flathead Subbasin Summary                     99                                  3/6/01
1.7) Purpose (Goal) of program(s).
    The goal of this program is to mitigate for Hungry Horse Dam hydro-related losses of
    415,000 salmonids annually from Flathead Lake by partially offsetting lost angler opportunity
    and reducing pressure on native stocks.

1.8)   Justification for the program.
       Stocking of small lakes and reservoirs isolated within the interconnected waters of the
       Flathead subbasin with 3-4‖ hatchery produced fish will, after one to two years growth,
       provide recreational angling opportunities for catchable sized trout and partially offset the
       affects of fishing closures and reduced limits on weak but recoverable native populations
       of Westslope cutthroat and bull trout remaining in the Flathead Lake and River system.

       Research into culture and biology of hatchery-reared bull trout benefits the listed
       populations through increased knowledge that may be useful in future restoration
       activities, and by reducing the need to take individuals from wild stocks.

1.9)   List of program “Performance Standards.”

   1. Provide predictable, stable and increased recreational harvest opportunity for westslope
   cutthroat trout and rainbow trout to help mitigate for native fisheries lost due to construction
   and operation of Hungry Horse Dam

       2. Enhance tribal, local, and state economies.

       3. Conduct within hatchery research and provide eggs to researchers to increase our
       knowledge of listed bull trout culture and biology.

1.10) List of program “Performance Indicators,” designated by "benefits" and "risks."

       1.10.1) “Performance Indicators” addressing benefits.
              The offsite lakes program is monitored through periodic gill net surveys, angler
              interviews and the annual statewide angler creel census. Stocking rates are
              established to a large degree by trial and error. Gill netting provides data on
              species relative abundance, growth rates and fish condition factor. Angler surveys
              are qualitative indicators of catch rates, angler satisfaction and rough estimates of
              harvest. Although rigorous quantitative analyses of CPUE, survival and total
              harvest are possible, the number of lakes involved makes this level of monitoring
              economically impractical. Rigorous sampling is reserved for aspects of the
              Hungry Horse mitigation program directed toward native species restoration.
              Listed bull trout are not present in any of the small, closed-basin waters stocked
              under this program, but are benefited through shifting of angler harvest away from
              natural but weak bull trout and westslope cutthroat trout populations.


Flathead Subbasin Summary                      100                                    3/6/01
              Evaluate performance of listed bull trout in artificial production; feed
              requirements, growth rates, age at maturity, fecundity, effective lifespan of
              broodfish. Provide supply of good quality eyed eggs to partners researching
              biology of bull trout and collect information on results of this outside research.

       1.10.2) “Performance Indicators” addressing risks.
               No identified risks to native or listed species.

1.11) Expected size of program.
      Produce up to 100,000 – 3‖ hatchery cutthroat trout and up to 100,000 – 3‖ rainbow trout
      and stock fish to offsite mitigation waters as requested by management agencies. Provide
      up to 200,000 bull trout eggs for other research programs

       1.11.1) Proposed annual broodstock need (maximum number of fish).
              This program employs fish and eggs obtained from captive hatchery broodstocks
              only.

       1.11.2) Proposed annual fish release levels (maximum number) by life stage and
               location.
              Anticipated schedule for 2001, subject to change.

Life Stage               Release Location                         Annual Release Level
Eyed Eggs
Unfed Fry
Fry




Flathead Subbasin Summary                      101                                   3/6/01
Life Stage                Release Location                      Annual Release Level
Fingerling                Rogers Lake            (CTT)          15,000
                          Lion Lake                  ―           6,000
                          Bailey Lake                ―           4,000
                          McWhorter’s Pond              ―        2,400
                          Bootjack Lake              ―           1,000
                          Myron Lake                ―            1,500
                          Hidden Lakes               ―           2,500
                          McDonald Lake                 ―       10,000
                          St. Mary’s Lake               ―       20,000
                          Mission Lake              ―           10,000
                          Turtle Lake               ―            2,000
                          Upper Jocko Res.           ―           3,000
                          Lower Jocko Res               ―        7,000
                          Upper Twin Lake               ―        2,000
                          Lower Twin Lake               ―        2,000
                          Swartz Lake               ―            5,000
                          Pablo Res.               RBT          20,000
                          McDonald Ponds                ―        5,000
                          Rainbow-Dog Lake              ―       10,000
Yearling

1.12) Current program performance, including estimated survival rates, adult production
       levels, and escapement levels. Indicate the source of these data.
       Qualitative assessments have shown that small, closed basin lakes yield an efficient
       hatchery plant to angler creel ratio. Project lakes are put, grow and take fisheries, entirely
       dependent on artificial production to support the fishery. Many have been chemically
       rehabilitated to remove illegally introduced species (e.g. yellow perch, bluegill,
       pumpkinseed, northern pike etc.). Gill netting, site visits to interview anglers and an
       annual statewide angler creel census provide managers with qualitative information on
       species composition, growth, condition factor and angling success. The number of lakes
       involved precludes detailed assessments of survival rates, total harvest or reliable
       estimates of CPUE. Periodic spot checks at individual lakes have revealed great success.
Flathead Subbasin Summary                        102                                   3/6/01
       For instance, angler pressure on Lion Lake grew to the highest of any small lake in
       northwest Montana. Rogers Lake now supports a genetic reserve for Red Rocks Lake
       fluvial grayling and a major fishery for westslope cutthroat trout (Knotek et al. 1997).

1.13) Date program started (years in operation), or is expected to start.
      Stocking of offsite waters under this program began in 1998.

1.14) Expected duration of program.
      Duration is permanent for foreseeable future.

1.15) Watersheds targeted by program.
      Offsite fish stocking to the Flathead sub-basin.
      Findings of bull trout research are applicable over fishes’ entire range.

1.16) Indicate alternative actions considered for attaining program goals, and reasons
      why those actions are not being proposed.
      Mitigation stocking of Westslope cutthroat trout directly into Flathead Lake was deemed
      not feasible due to probable heavy predation by non-native lake trout. This is based on the
      results of the attempted kokanee salmon reintroductions of 1992-1997.

SECTION 2. RELATIONSHIP OF PROGRAM TO OTHER MANAGEMENT OBJECTIVES

2.1)   Describe alignment of the hatchery program with other hatchery plans and policies
       (e.g., the NPPC Annual Production Review Report and Recommendations - NPPC
       document 99-15). Explain any proposed deviations from the plan or policies.
       All hatchery fish rearing and stocking and bull trout egg production is consistent with the
       NPPC Artificial Production Review document 99-15, and with USFWS fish health,
       genetics, and distribution plans and policies. The program will align with the Flathead
       sub-basin summary.

2.2)   List all existing cooperative agreements, memoranda of understanding, memoranda
       of agreement, or other management plans or court orders under which the program
       operates.
       This program is a part of, and consistent with the Hungry Horse Dam Fisheries Mitigation
       Plan, an agreement between the Service, the Montana FWP, and the CSKT which was
       implemented in 1992.

2.3)   Relationship to harvest objectives.
       Hatchery produced fish are stocked in closed basin lakes with no reproduction potential to
       provide harvest and recreational opportunities for anglers, and reduce fishing pressure on
       natural populations. There are no risks to natural populations.



Flathead Subbasin Summary                      103                                   3/6/01
       2.3.1) Describe fisheries benefiting from the program, and indicate harvest levels
              and rates for program-origin fish for the last 12 years (1988-99), if available.
              The offsite lakes program balances public desire for harvestable fisheries for
              rainbow and westslope cutthroat trout. The number of lakes involved precludes
              detailed assessments of harvest levels and rates. Angler preference and pressure
              can be assessed through the annual statewide creel census.

2.4)   Relationship to habitat protection and purposes of artificial production.
       Nearly all of the offsite lakes planted under this program do not support natural
       reproduction. Where natural reproduction is possible, the primary objective is to create
       genetic reserves for isolated populations of native stocks. In these cases, habitat
       restoration is performed to enhance fish passage and natural reproduction in the closed
       system, and hatchery produced fish are not utilized. Hatchery production placed in lakes
       lacking reproductive habitat helps to mitigate for good habitat permanently blocked by
       Hungry Horse Dam.

2.5)   Ecological interactions.
       This program does not supply fish to waters scheduled for native species restoration. The
       closed basin lakes that are stocked through this program provide alternative fisheries to
       meet public demands for harvest and partially offset fishing bans or reduced limits
       enacted for native species recovery. This program may indirectly benefit native species
       recovery by redirecting harvest away from sensitive recovery areas in the contiguous
       Flathead watershed. Rehabilitated lakes remove undesirable species that are a source for
       additional illegal introductions (e.g. illegally introduced yellow perch, northern pike,
       sunfish, fathead minnow and in one case, grass carp). Occasionally, illegal introductions
       occur after lakes have been reclaimed and fisheries established. This negatively impacts
       the program. An additional chemical treatment may be required within approximately ten
       years. During the interim, fisheries established by this program remain viable until the
       undesirable introduced fish become reestablished.


SECTION 3. WATER SOURCE

3.1)   Provide a quantitative and narrative description of the water source (spring, well,
       surface), water quality profile, and natural limitations to production attributable to
       the water source.
       The Creston NFH has non-consumptive water rights on natural springs with flows
       ranging from 12,000 to 18,000 gpm, depending on the season and rainfall totals. The
       springs are a constant 47 F, but the water is warmed or cooled (depending on season) by a
       24-acre man-made impoundment (Jessup Mill Pond) before entering the hatchery. Annual
       range is 39F to 52F. The water is well oxygenated (10ppm) and slightly basic (pH-7.6).
       The water does become nitrogen gas supersaturated (as high as 130%) during periods
       when the water temperature is above 45F (March through October). This causes a chronic
Flathead Subbasin Summary                     104                                  3/6/01
       stress to all fish species reared, but cutthroat trout are more susceptible than others.
       Bacterial infections causing various diseases and some loss of fish can occur. The
       hatchery is equipped with aeration columns to degas water supplying a quarter of the
       rearing space, and cutthroat and bull trout are held in these areas.

       The hatchery building, where egg incubation, hatching, and early rearing takes place,
       makes use of a 260’ deep- 14‖ diameter well that has an artesian flow of 190 gpm, and
       sustained pumping flow of 600 gpm. Water is aerated to 10 ppm oxygen, and nitrogen gas
       is not a problem. Temperature is a constant 47F. The spring source water described in the
       previous paragraph is not assured to be disease free, and since 1995 has not been used in
       the hatchery.

       The isolation room, located on one end of the feed storage building, is supplied by a 200’
       deep – 6‖ diameter well with useable 10 gpm artesian flow and 100 gpm pumped flow. A
       chiller unit cools the 47F water to levels suitable for incubating bull trout eggs (39-42F).

3.2)   Indicate any appropriate risk aversion measures that will be applied to minimize
       the likelihood for the take of listed species as a result of hatchery water withdrawal,
       screening, or effluent discharge.
       Listed fish such as bull trout are not present in Jessup Mill Pond nor are they found in
       Mill Creek on or below the hatchery. Bull trout occasionally enter Mill Creek from the
       Flathead River (6 miles downstream) it is not, and historically was not, bull trout
       spawning habitat.

SECTION 4. FACILITIES

4.1)   Broodstock collection, holding, and spawning facilities .
       The bull trout captive broodstock are held in two 8’x 80’ x 2.5’ concrete raceways
       receiving 325 gpm each of Jessup Mill Pond water. The raceways are completely covered
       with a vinyl shelter tent. The fish are manually spawned in the raceways.

4.2)   Fish transportation equipment (description of pen, tank truck, or container used).
       Rainbow and cutthroat trout stocked under this program are transported in either a 1991
       Ford F-800 diesel truck with three –500 gallon fiberglass tanks mounted to the frame, or
       in a two-compartment 400 gallon fiberglass tank carried in box of a 1994 Chevy ¾ ton
       pickup. All tanks are supplied with ceramic air stones for oxygen, and aerators for water
       circulation.

43)    Incubation facilities.
       Bull trout eggs are incubated in Heath-Tray type incubators located in the isolation room
       mentioned in 3.1 above. After reaching the eyed stage, eggs are shipped via Fed Ex to
       various researchers.


Flathead Subbasin Summary                      105                                    3/6/01
       Eyed cutthroat and rainbow trout eggs received from other facilities are placed in 8‖ dia.
       x 22‖ high custom-made PVC egg jars located in early rearing tanks in main hatchery
       building. After hatching, the sac-fry may hold within the jars or volitionally flow from the
       jars directly into the rearing tanks

4.4)   Rearing facilities.
       Early rearing occurs in twenty-three 12’x3’x2’ tanks (capacity approx. 72 cubic feet)
       located in hatchery tank room. Sixteen of the tanks are concrete and seven are fiberglass
       and were installed in 1992. Fish are reared in these units until at least 2‖ in length.
       Fish over 2‖ long are placed in outdoor concrete raceways measuring 8’ x 80’ x 2.5’.
       Spring water for twelve of the raceways is gravity fed through 6’ degassing columns to
       remove supersaturated nitrogen gases. Eight of these 12 are covered with vinyl tent
       enclosures. Another 24 raceways are not covered and do not have nitrogen degassing
       capability, but are covered with netting to keep predatory birds out. An additional 12
       raceways are currently not useable. Water flow rates are usually set at 300-350 gpm per
       raceway, single pass only.

4.5)   Acclimation/release facilities.
       None

4.6)   Describe operational difficulties or disasters that led to significant fish mortality.
       None

       4.6.1) Indicate available back-up systems, and risk aversion measures that
              minimize the likelihood for the take of listed species that may result from
              equipment failure, water loss, flooding, disease transmission, or other events
              that could lead to injury or mortality.
              Water flow to bull trout broodfish is all gravity flow. Water supply to incubating
              bull trout eggs is via artesian well. Loss of flow is not possible except in event of
              major natural disaster.
              To help prevent spread of fish pathogens, raceway cleaning brushes used for bull
              trout brood (and all fish on hatchery) are not used interchangeably with other
              units, and are disinfected after each use.
              Incubating bull trout eggs are housed in isolation unit to minimize contact with
              fish pathogens that may be present in other areas of hatchery.
              Hatchery is staffed 7 days a week.

       4.6.2) Indicate needed back-up systems and risk aversion measures that minimize
              the likelihood for the take of listed species that may result from equipment
              failure, water loss, flooding, disease transmission, or other events that could
              lead to injury or mortality.



Flathead Subbasin Summary                      106                                    3/6/01
              A high fence would need to be placed around raceways housing bull trout
              broodfish to absolutely ensure their safety from vandals and illegal fishermen
              during hours of darkness.

SECTION 5. BROODSTOCK ORIGIN AND IDENTITY

5.1)   Source.
       Bull trout broodstock are progeny of wild fish captured, artificially spawned, and released
       in Holland Creek, a tributary of the Swan River, a major drainage of the Flathead basin.
       Westslope cutthroat trout eggs are supplied from broodstocks held at the Washoe Park
       State Fish Hatchery, in Anaconda, MT. Original source of this broodstock was genetically
       pure wild fish found in tributaries of the South Fork of the Flathead River (Hungry Horse
       Reservoir).
       Arlee strain rainbow trout eggs are supplied from broodfish held at the Ennis National
       Fish Hatchery, Ennis, MT.

5.2)   Supporting information.
       5.2.1) History.
              The existing hatchery bull trout broodstock were originally collected as eggs from
              7 wild females (mated one on one) in the Swan River drainage of NW Montana in
              September 1993. About 21,000 eggs were collected. In 1996, we randomly
              selected 400 of these bull trout to keep for captive broodstock investigations,
              while all remaining surplus fish were stocked into Duck Lake on the Blackfoot
              Indian Reservation. Due to the small number of founding parents, no attempt has
              been made to perpetuate this broodstock. It will eventually die out.

       5.2.2) Annual size.

              N.A.

       5.2.3) Past and proposed level of natural fish in broodstock.

              None

       5.2.4) Genetic or ecological differences.

              None known

       5.2.5) Reasons for choosing Broodstock traits

              N.A.

       5.2.6) ESA-Listing status
Flathead Subbasin Summary                     107                                   3/6/01
              Bull trout are listed as a threatened species. Westslope cutthroat trout were
              petitioned for listing, but listing was deemed not warranted by the USFWS.

5.3)   Indicate risk aversion measures that will be applied to minimize the likelihood for
       adverse genetic or ecological effects that may occur as a result of using the
       broodstock source.

       N.A.

SECTION 6. BROODSTOCK COLLECTION

6.1)   Life-history stage to be collected ( eggs, juveniles, adults).
       N.A.

6.2)   Collection or sampling design.
       Adult bull trout were captured with dip nets during their spawning run up Holland Creek,
       a small stream inlet to Holland Lake located in the Swan River drainage of the Flathead
       basin. Seven females were captured in 1993, and 3 females in 1994. Fish were
       anesthetized before egg collection began. The fish were only partially spawned and
       returned to the stream unharmed. Eggs were fertilized 1:1 with males captured at the
       same time.

6.3)   Identity.

   All bull trout spawned during the 1993 & 1994 egg takes were from a natural population. No
   hatchery origin fish were or are now present in the population.

6.4)   Proposed number to be collected:
       None

       6.4.1) Program goal (assuming 1:1 sex ratio for adults):
              N.A.

       6.4.2) Broodstock collection levels for the last 12 years (e.g., 1988-99), or for
              most recent years available:




Flathead Subbasin Summary                      108                                  3/6/01
Year           Adults
                Females            Males            Jacks   Eggs               Juveniles
1988
1989
1990
1991
1992
1993                                                        20,800
1994                                                        12,000
1995
1996
1997
1998
1999
Data source: (Link to appended Excel spreadsheet using this structure. Include hyperlink to main
database)

6.5) Disposition of hatchery-origin fish collected in surplus of broodstock needs.
    N.A.

6.6) Fish transportation and holding methods.
    N.A.


6.7)   Describe fish health maintenance and sanitation procedures applied.
       Bull trout brood fish are treated for occasional bacterial infections when they occur;
       usually during periods of higher stress such as after spawning season, or in early spring
       when water temperature begins to rise. Fish are treated with oxytetracycline at 1.44% of
       diet for 10 days, or Romet-30 at 2% of diet for 10 days to clear up infection.
       Cleanliness is maintained by daily sweeping of raceway floors with nylon/steel bristled
       brushes to remove waste products and excess feed.

6.8) Disposition of carcasses.
    N.A.


Flathead Subbasin Summary                     109                                   3/6/01
6.9)  Indicate risk aversion measures that will be applied to minimize the likelihood for
      adverse genetic or ecological effects to listed species resulting from the broodstock
      collection program.
   N.A.

SECTION 7. MATING
Describe fish mating procedures that will be used, including those applied to meet
performance indicators identified previously.


7.1)   Selection method.
        All egg-producing bull trout females from the hatchery broodstock are spawned when
       ripe.

7.2) Fertilization.
    Ripe eggs are stripped from anesthetized (MS-222) female bull trout using air spawning
    technique (2 psi oxygen introduced into body cavity via needle to force egg expulsion). Eggs
    from 5 females are pooled in pan containing 1.5% saline solution and are fertilized with
    pooled milt pre-collected from 5 males. To remove any external pathogens, newly fertilized
    eggs are water hardened in 0.75% iodine solution for 60 minutes prior to placement in
    incubation trays.

7.3) Cryopreserved gametes.
    N.A.

7.4)   Indicate risk aversion measures that will be applied to minimize the likelihood for
       adverse genetic or ecological effects to listed natural fish resulting from the mating
       scheme.
       N.A.

SECTION 8. INCUBATION AND REARING

8.1)   Incubation:
       8.1.1) Number of eggs taken/received and survival rate at stages of egg development




Flathead Subbasin Summary                     110                                  3/6/01
      Bull trout eggs taken by USFWS personnel.

      Year                 # of eggs               % to eyeup           % to hatch
                    Wild          Captive
      1993          20,800                         97.4                 97.1
      1994          12,000                          ?                     ?
      1997                        71,641           70.5                 55.4
      1998                       201,183           76.0                 shipped
      1999                       155,474           67.4                 shipped
      2000                       136,037            ?                   shipped


      Westslope cutthroat trout eyed eggs received from Washoe Park State Fish Hatchery,
      Anaconda, Montana. (captive broodstock)

      Year          # eyed eggs received                  % to hatch

      1997                  366,472                             81.8
      1998                  212,517                             68.2
      1999                  339,254                             84.9
      2000                  300,734                             84.8


      Arlee strain rainbow trout eggs received from Ennis National Fish Hatchery, Ennis,
      Montana.

         Year               # eyed eggs received          % to hatch

      1997                  118,030                             84.7
      1998                  119,180                             75.5
      1999                  111,354                             93.4




Flathead Subbasin Summary                   111                                   3/6/01
      8.1.2) Loading densities applied during incubation.

      Bull trout eggs incubated in Heath trays

      Year           Egg Size (#/oz)       Flow Rate (gpm)        # Eggs/Tray

      1997             360                   3.3                   11,940
      1998             337                   5.0                   28,740
      1999             287                   4.5                   25,912
      2000             263                   3.8                   17,005


      Westslope cutthroat trout eyed eggs incubated in hatching jars (Vol.=1000 cubic inches).

      Year           Egg Size (#/0z)       Flow Rate (gpm)        # Eggs/Jar
                                              Per Jar

      1997             372                         5.0             52,285
      1998             381                         5.0             42,503
      1999             340                         5.0             48,464
      2000             417                         5.0             35,385


      Arlee rainbow trout eyed eggs incubated in hatching jars (Vol=1000 cubic inches).

      Year           Egg Size (#/oz)         Flow Rate            # Eggs/Jar
                                             Per Jar (gpm)

      1997               290                       5.0               39,343
      1998               296                       5.0               39,726
      1999               277                       5.0               37,118


      8.1.3) Incubation conditions.
              For bull trout:
              Chilled incubation water averages 5.8C , fluctuating less than +/- 1C as chiller
              cycles on and off. Water is pumped from well and dropped through
              aeration/degassing column before entering chiller. Oxygen monitoring is not
              necessary, concentration is 9.5 to 10.2 ppm. Eggs incubated in 8-tray Heath stack.




Flathead Subbasin Summary                    112                                  3/6/01
              For rainbow and cutthroat:
              Artesian flow well water averaging 47F, falls through aeration column and enters
              hatchery. Oxygen concentration is 10.0 to 10.5 ppm. Eyed eggs incubated and
              hatched in 8‖ dia x 20‖ long PVC jars with upwelling flow.


       8.1.4) Ponding.
              Bull trout fry from the 1993 and 1994 wild spawn takes were removed from
              incubator trays and placed in rearing troughs at time of yolk-sac absorption. This
              occurred in early March, approx. 6 months after spawning.

              Westslope cutthroat fry volitionally leave hatching jars and directly enter 72 cubic
              foot concrete hatchery rearing tanks (in late July). Depending on hatchery space,
              the fish may be moved to outdoor raceways in January (when 2‖ in length), or
              remain in hatchery tanks until stocked in May or June.

              Rainbow fry also volitionally leave hatching jars and enter rearing tanks (in late
              January), and are moved to outdoor raceways in May after they attain 2‖ length.

       8.1.5) Fish health maintenance and monitoring.
              Incubating bull trout eggs are treated with a 1:600 formaldehyde solution for 15
              minutes every other day for control of Saprolegnia spp. After eye-up, eggs are
              lightly shocked, and dead eggs are hand picked with a suction bulb every other
              day.

              Eyed eggs of rainbow and cutthroat trout do not require chemical treatments in the
              later stages of incubation in hatching jars. Dead eggs or fry are removed daily with
              hand pickers before, during, and after hatching takes place.

       8.1.6) Indicate risk aversion measures that will be applied to minimize the
              likelihood for adverse genetic and ecological effects to fish during
              incubation.
              There would be no adverse genetic or ecological effects to environment caused by
              loss of incubating eggs from any of these three species. Escape of bull trout eggs
              or fry from isolation room to environment is not possible due to fish containment
              system in place.

8.2)   Rearing:
       8.2.1) Provide survival rate data (average program performance) by hatchery life
              stage (fry to fingerling; fingerling to release) for the most recent twelve years
              (1988-99), or for years dependable data are available..



Flathead Subbasin Summary                     113                                   3/6/01
                            Bull Trout survival
             Year           % fry to fingerling           % fingerling to release

             1994                  95.2                          66.5
             1995                  no data


                            Westslope cutthroat trout survival
             Year           % fry to fingerling           % fingerling to release

             1998                  60.7                          80.9
             1999                  74.1                          68.6
             2000                  67.7                          74.6


                            Arlee rainbow trout survival
             Year           % fry to fingerling          % fingerling to release

             1998                  88.2                          67.9
             1999                  91.1                          62.1
             2000                  93.4                          98.0



      8.2.2) Density and loading criteria (goals and actual levels).

             The maximum desirable Flow Index for Creston NFH is 1.56; where permissible
             weight of fish=1.56 X fish length (inches) X inflow (gpm).
             The maximum Flow Index attained with Westslope cutthroat trout was 1.0 in
             June, 2000.
             The maximum attained with Arlee rainbow trout was 1.29 in June 2000.

             The maximum Density Index desirable at Creston is 0.5; where permissible
             weight of fish=0.5 X Volume of tank (cubic feet) X fish length (inches).
             The maximum density index attained with Westslope cutthroat trout was 0.14 in
             June, 2000.
             The maximum attained with Arlee rainbow trout was 0.29 in June, 2000.

      8.2.3) Fish rearing conditions

             Constant water temperature recordings at Creston NFH indicate an annual
             temperature range from 39F to 52F, with an average temperature of 47F.
             Minimum dissolved oxygen readings at tailscreens range from 8 to 9 ppm, and are

Flathead Subbasin Summary                    114                                    3/6/01
             measured only occasionally. Total gas pressure (TGP) is below saturation during
             colder months, (November to March) but becomes supersaturated during times of
             warmer temperatures. A high of 108% to 112% is attained in late spring, causing
             some chronic stress and low mortality to fish exposed to such. Degassing columns
             were installed in 1992 to treat water supplying lower 12 raceways. TGP will run
             <103% with columns operated in open mode, and below 100% in closed mode
             with oxygen injection. Koch ring media in columns are replaced once a year.
             Westslope cutthroat trout are very susceptible to higher gas pressures and are
             either reared inside the hatchery building, where TGP remains <101%, or in the
             raceways receiving treated water. Rainbow trout are lightly affected by the high
             TGP.
             To help prevent disease, all empty raceways are thoroughly cleaned and sanitized
             with a high-pressure washer before restocking with fish. The upper 24 raceways
             are covered with bird netting, which helps prevent stress and losses to herons,
             ducks, and osprey. Eight of the lower raceways have shelter covers which
             provides shade and helps to keep birds out. However, mink and kingfishers do
             account for some predation.

      8.2.4) Indicate biweekly or monthly fish growth information (average program
             performance), including length, weight, and condition factor data collected
             during rearing, if available.
             Sample counts (#/lb.) are made when fish are moved to other rearing units, or
             hauled off the hatchery for stocking. Condition factors are not measured directly
             in most cases. Lengths are estimated from standard species condition factor charts.

             Monthly temperature units (T.U.) growth data from 3 year classes of Westslope
             cutthroat trout indicates an average of 67 T.U.’s per inch growth. (1 T.U. = 1
             degree above freezing for 30 days)

             For Arlee rainbow trout, the 3 year average was 29 T.U.’s per inch growth.

             The average number of T.U.’s available annually at Creston NFH is 169.


      8.2.5) Indicate food type used, daily application schedule, feeding rate range (e.g.
             % B.W./day and lbs/gpm inflow), and estimates of total food conversion
             efficiency during rearing (average program performance).

             Cutthroat trout are started on Biodiet starter #1 and #2 and then are fed the
             USFWS specification trout diet (dry feed), milled by either Silver Cup or
             Rangens. Rainbow trout are fed the dry Service diet only. Bull trout broodstock
             are fed the dry Service brood diet.


Flathead Subbasin Summary                    115                                  3/6/01
             About 1/3 to ½ of daily feed is applied through 12-hour belt feeders, (Two per
             raceway, one per hatchery tank) with the rest hand broadcast 3 times a day. Fish
             are fed to about 95% of satiation.

             The 3-year average feed conversion (food fed/weight gain) for Westslope
             cutthroat trout is 1.53, for Arlee rainbow trout it is 0.98.


      8.2.6) Fish health monitoring, disease treatment, and sanitation procedures.
             Fish are sampled annually for disease pathogens by the USFWS Bozeman Fish
             Health Lab. Sixty fish are sacrificed from each lot located on the station and
             tissues are tested for whirling disease, bacterial and viral infections. Moribund
             fish may be sent to the lab anytime for inspection if an epizootic is in progress.

             Westslope cutthroat trout must be treated for bacterial ―coldwater disease‖
             (Flexibactor spp) soon after swimup, and as outbreaks occur later. They are
             treated with 4% oxytetracycline in the diet for 10 days to control the disease.
             Other species reared at Creston are not affected. Outbreaks of bacterial gill
             disease (Aeromonas or Psuedomonas spp) , caused by overfeeding or
             overcrowding, are rare, but are controlled by adding 12ppm chloramine-t to the
             water for one hour, every other day for 3 days.

             To maintain good sanitation, hatchery tanks are cleaned with brushes twice a day
             and outdoor raceways once a day, to remove uneaten feed and fecal matter. Each
             hatchery tank has its own cleaning brush, which is not used interchangeably with
             other tanks. Outdoor raceway brushes are placed in nearby tubs containing a
             sterilizing solution after each use.
              Pathogen-free well water only is used in the hatchery building. Footbaths and
             handwashing are required before entering the tank room.
             And, as stated before, empty raceways are cleaned with a high pressure sprayer
             (4000 psi) before the next use.

      8.2.7) Indicate the use of "natural" rearing methods as applied in the program.
             All rearing units at the Creston NFH are made of concrete or fiberglass.

      8.2.8) Indicate risk aversion measures that will be applied to minimize the
      likelihood for adverse genetic and ecological effects to fish under propagation.
              None employed.




Flathead Subbasin Summary                     116                                   3/6/01
SECTION 9. RELEASE
Describe fish release levels, and release practices applied through the hatchery program.

9.1)   Proposed fish release levels. (Use standardized life stage definitions by species
       presented in Attachment 2. “Location” is watershed planted (e.g., “Elwha River”).
Age Class          Maximum             Size (fpp)           Release Date   Location
                   Number
Eggs
Unfed Fry
Fry
Fingerling         100,000 wes. CTT 115/lb                  May-June       Flathead River
                   100,000 RBT      50/lb                   June-July      Flathead River


Yearling

9.2)   Specific location(s) of proposed release(s).
       Stream, river, or watercourse: All waters listed in Sec. 1.11.2
       Release point:
       Major watershed: Flathead River
       Basin or Region: Columbia River Basin/Mountain Columbia Province

9.3)   Actual numbers and sizes of fish released by age class through the program.
       Source:   Creston National Fish Hatchery, fish distribution records.
Release Eggs/     Avg size Fry          Avg size Fingerling Avg size Yearling      Avg size
year    Unfed Fry




                                                    Arlee       RBT
1998                                                34,964      16.33
1999                                                50,938      19.08
2000                                                38,976      8.10

Flathead Subbasin Summary                   117                                 3/6/01
Release Eggs/     Avg size Fry                   Avg size Fingerling Avg size Yearling                 Avg size
year    Unfed Fry


                                                              Westslope CTT
1998                                                           101,175      6.40
1999                                                           63,653       7.44          2,834        34.9
2000                                                           94,838       3.93
Average

9.4)      Actual dates of release and description of release protocols.

    Fingerling fish are stocked when receiving waters have reached a suitable temperature, (50-55F) generally mid-
May to mid-June. Fish are transported to the lakes via tank truck.

9.5) Fish transportation procedures, if applicable.
    A fish pump is used to lift fish into a dewatering box, from which they enter the distribution
    truck tanks via a chute. Fish are enumerated by water displacement in the tanks. Oxygen is
    metered from a liquid O2 tank at the rate of 1 lpm per 100 lb of fish, through ceramic stones
    into tanks. Each tank has 3 aerator pumps for water circulation and CO2 dispersal.
    Temperature increase is minimal in the insulated fiberglass tanks. Cutthroat densities are kept
    below ½ lb/gal, and rainbow densities are no more than 1.5 lb/gal. Fish may remain in transit
    for 1 to 6 hours, depending upon destination and number of lakes stocked.

9.6)      Acclimation procedures
          Acclimation procedures are not necessary.

9.7)      Marks applied, and proportions of the total hatchery population marked, to identify
          hatchery component.
          None

9.8)      Disposition plans for fish identified at the time of release as surplus to programmed
          or approved levels.
          There have been no excess cutthroat so far, and none are expected. In 2000, excess
          rainbows were provided to state managed recreational waters within the Flathead
          subbasin.

9.9)      Fish health certification procedures applied pre-release.
          Each lot of fish reared at the Creston NFH is sampled annually for disease status by
          personnel of the USFWS Bozeman Fish Health Center.


Flathead Subbasin Summary                               118                                         3/6/01
9.10) Emergency release procedures in response to flooding or water system failure.
      Creston has a gravity flow water supply. Spring flow is dependable year-round between
      12,000-18,000 gpm. The watershed is too small to experience a flood event. However, the
      dam holding back Jessup mill pond is unstable and could fail during a large earthquake.
      A design is now being formed to either repair the dam, or drain the pond and enclose the
      hatchery supply springs in pipeline. Service funds have been appropriated, and
      construction will take place in 2002.

9.11) Indicate risk aversion measures that will be applied to minimize the likelihood for
      adverse genetic and ecological effects to listed species resulting from fish releases.
      Fish stocked under this program are no threat to listed species (bull trout).

SECTION 10. PROGRAM EFFECTS ON ALL ESA-LISTED, PROPOSED,
AND CANDIDATE SPECIES (FISH AND WILDLIFE)

10.1) List all ESA permits or authorizations in hand for the hatchery program.

       DOI-USFWS Federal Fish and Wildlife Permit PRT-704930, subpermit sp98-37.00
       Allows all hatchery activities associated with bull trout described in this plan

10.2) Provide descriptions, status, and projected take actions and levels for ESA-listed
      natural populations in the target area.
      None under this program.

       10.2.1) Description of ESA-listed, proposed, and candidate species affected by the
               program.
               None

              Identify the ESA-listed population(s) that will be directly affected by the
              program.

              One time affect on bull trout in several years pre-listing (1993&1994) through
              take of approximately 33,000 eggs from natural Swan drainage bull trout
              population.

              - Identify the ESA-listed population(s) that may be incidentally affected by
              the program.
              None




Flathead Subbasin Summary                    119                                  3/6/01
       10.2.2) Status of ESA-listed species affected by the program.

               - Describe the status of the listed natural population(s) relative to “critical”
               and “viable” population thresholds (see definitions in “Attachment 1").
               NA

               - Provide the most recent 12 year (e.g. 1988 - present) progeny-to-parent
               ratios, survival data by life-stage, or other measures of productivity for the
               listed population. Indicate the source of these data.
               NA

               - Provide the most recent 12 year (e.g. 1988 - 1999) annual spawning
               abundance estimates, or any other abundance information. Indicate the
               source of these data.
               NA

        - Provide the most recent 12 year (e.g. 1988 - 1999) estimates of annual proportions of
direct hatchery-origin and listed natural-origin fish on natural spawning grounds, if known.
                NA

       10.2.3) Describe hatchery activities, including associated monitoring and evaluation
               and research programs, that may lead to the take of listed species in the
               target area, and provide estimated annual levels of take (see “Attachment 1"
               for definition of “take”). Provide the rationale for deriving the estimate.
               None

               - Describe hatchery activities that may lead to the take of listed species in the
               target area, including how, where, and when the takes may occur, the risk
               potential for their occurrence, and the likely effects of the take.
               None

               -Provide information regarding past takes associated with the hatchery
               program, (if known) including numbers taken, and observed injury or
               mortality levels for listed fish.
               Take of 20,000 fertilized eggs in 1993 and 12,800 fertilized eggs in 1994 from
               total of 10 wild female bull trout in the Swan River drainage. No observed injury
               or mortality to adults resulted from spawn take operation.

               - Provide projected annual take levels for listed species by life stage (juvenile
               and adult) quantified (to the extent feasible) by the type of take resulting
               from the hatchery program (e.g. capture, handling, tagging, injury, or lethal
               take).
               None
Flathead Subbasin Summary                      120                                  3/6/01
              Indicate contingency plans for addressing situations where take levels within
              a given year have exceeded, or are projected to exceed, take levels described
              in this plan for the program.
              NA


SECTION 11. MONITORING AND EVALUATION OF PERFORMANCE
INDICATORS

11.1) Monitoring and evaluation of “Performance Indicators” presented in Section 1.10.

       11.1.1) Describe the proposed plans and methods necessary to respond to the
               appropriate “Performance Indicators” that have been identified for the
               program.
               The offsite lakes program is monitored by the responsible management agencies
               (MDFWP and CSKT) through periodic gill net surveys, angler interviews and the
               annual statewide angler creel census. Stocking rates are established to a large
               degree by trial and error. Gill netting provides data on species relative abundance,
               growth rates and fish condition factor. Angler surveys are qualitative indicators of
               catch rates, angler satisfaction and rough estimates of harvest.

       11.1.2) Indicate whether funding, staffing, and other support logistics are available
               or committed to allow implementation of the monitoring and evaluation
               program.
               The USFWS is not directly involved in monitoring the offsite lakes stocking
               program. Monitoring is performed by the agencies responsible for management of
               the waters. They are Montana Fish, Wildlife, and Parks Dept. for state waters in
               the portion of the Flathead drainage above Flathead Lake; and the Confederated
               Salish and Kootenai Tribes for waters within the Flathead Indian Reservation
               (below Flathead Lake). These agencies receive sufficient funding through this
               process to implement monitoring programs on these stocked waters.

11.2) Indicate risk aversion measures that will be applied to minimize the likelihood for
      adverse genetic and ecological effects to listed species resulting from monitoring and
      evaluation activities.
      None of the waters stocked under this mitigation program contain self-sustaining natural
      populations of listed and/or native fishes. Therefore, monitoring activities conducted on
      these waters do not genetically or ecologically impact those species.

SECTION 12. RESEARCH
Provide the following information for any research programs conducted in direct association
with the hatchery program described in this HGMP. Provide sufficient detail to allow for the
Flathead Subbasin Summary                     121                                 3/6/01
independent assessment of the effects of the research program on listed fish. Attach a copy of any
formal research proposal addressing activities covered in this section. Include estimated take
levels for the research program with take levels provided for the associated hatchery program in
Table 1.

12.1) Objective or purpose.

       Purpose was to develop fish culture techniques for bull trout, (feeding methods, diets,
       cover requirements, etc.) in the event it becomes desirable or necessary in the future to
       artificially rear bull trout for restoration or refugia purposes.
            Currently, eggs produced from the broodstock established from the 1993 wild egg
       take have been used in a variety of research endeavors, such as; a 3 yr. blood hormone
       bioassay; hybridization experiments with dolly varden; susceptibility to whirling disease;
       sensitivity to heavy metals, dioxins, and PCB; screening criteria for bull trout; and
       optimal and lethal thermal criteria for growth and survival; and preserved reference sets
       of early life stages for field identification use. This information will greatly aid in the
       recovery efforts of this listed species.

12.2) Cooperating and funding agencies.
      Funding for this project provided by the BPA through the Hungry Horse Fisheries
      Mitigation Plan.
         Agencies utilizing our bull trout in their research has included the Oregon DFW;
      Univ. of B.C.; Univ. of Wyo.; Montana DFWP; USEPA-Duluth; and the USFWS’s
      Bozeman and Abernathy Fish Tech Centers.

12.3) Principle investigator or project supervisor and staff.
      Wade Fredenburg and Don Edsall of the USFWS Creston Fish & Wildlife Center oversee
      fish cultural observations at the Creston Hatchery.

12.4) Status of population, particularly the group affected by project, if different than the
      population(s) described in Section 2.
      NA

12.5) Techniques: include capture methods, drugs, samples collected, tags applied.
      NA

12.6) Dates or time period in which research activity occurs.
      Yearlong with hatchery produced fish.

12.7) Care and maintenance of live fish or eggs, holding duration, transport methods.
      NA



Flathead Subbasin Summary                      122                                  3/6/01
12.8) Expected type and effects of take and potential for injury or mortality.
      NA

12.9) Level of take of listed species: number or range of individuals handled, injured, or
      killed by sex, age, or size, if not already indicated in Section 2 and the attached
      “take table” (Table 1).
      None under current program.

12.10) Alternative methods to achieve project objectives.
       NA

12.11) List species similar or related to the threatened species; provide number and causes
       of mortality related to this research project.
       None

12.12) Indicate risk aversion measures that will be applied to minimize the likelihood for
       adverse ecological effects, injury, or mortality to listed species as a result of the
       proposed research activities.
       NA


SECTION 13. ATTACHMENTS AND CITATIONS
Include all references cited in the HGMP. In particular, indicate hatchery databases used to
provide data for each section. Include electronic links to the hatchery databases used (if
feasible), or to the staff person responsible for maintaining the hatchery database referenced
(indicate email address). Attach or cite (where commonly available) relevant reports that
describe the hatchery operation and impacts on the listed species or its critical habitat. Include
any EISs, EAs, Biological Assessments, benefit/risk assessments, or other analysis or plans that
provide pertinent background information to facilitate evaluation of the HGMP.


SECTION 14. CERTIFICATION LANGUAGE AND SIGNATURE OF
RESPONSIBLE PARTY
―I hereby certify that the foregoing information is complete, true and correct to the best of my
knowledge and belief. I understand that the information provided in this HGMP is submitted for
the purpose of receiving limits from take prohibitions specified under the Endangered Species
Act of 1973 (16 U.S.C.1531-1543) and regulations promulgated thereafter for the proposed
hatchery program, and that any false statement may subject me to the criminal penalties of 18
U.S.C. 1001, or penalties provided under the Endangered Species Act of 1973.‖




Flathead Subbasin Summary                      123                                   3/6/01
   Name, Title, and Signature of Applicant:

   Certified by_____________________________ Date:_____________



      Table 1. Estimated listed species take levels by hatchery activity.

Listed species affected: __________________________
ESU/Population:_________________________________ Activity:____________________
Location of hatchery activity:______________________ Dates of activity:____________________
Hatchery program operator:_________________
                                                        Annual Take of Listed Fish By Life Stage
                                                        (Number of Fish)
Type of Take
                                                        Egg/Fry     Juvenile/ Adult        Carcass
                                                                    Smolt
Observe or harass a)
Collect for transport b)
Capture, handle, and release c)
Capture, handle, tag/mark/tissue sample, and release d)
Removal (e.g. broodstock) e)
Intentional lethal take f)
 Unintentional lethal take g)
Other Take (specify) h)

      a. Contact with listed fish through stream surveys, carcass and mark recovery projects, or
      migrational delay at weirs.
      b. Take associated with weir or trapping operations where listed fish are captured and
      transported for release.
      c. Take associated with weir or trapping operations where listed fish are captured, handled
      and released upstream or downstream.
      d. Take occurring due to tagging and/or bio-sampling of fish collected through trapping
      operations prior to upstream or downstream release, or through carcass recovery programs.
      e. Listed fish removed from the wild and collected for use as broodstock.
      f. Intentional mortality of listed fish, usually as a result of spawning as broodstock.
      g. Unintentional mortality of listed fish, including loss of fish during transport or holding
      prior to spawning or prior to release into the wild, or, for integrated programs, mortalities
      during incubation and rearing.
      h. Other takes not identified above as a category.



   Flathead Subbasin Summary                       124                                  3/6/01
Instructions:
1. An entry for a fish to be taken should be in the take category that describes the greatest
impact.
2. Each take to be entered in the table should be in one take category only (there should
not be more than one entry for the same sampling event).
3. If an individual fish is to be taken more than once on separate occasions, each take
    must be entered in the take table




Flathead Subbasin Summary                    125                                     3/6/01
         Table 20. Flathead River Subbasin Summary FY 2002 - 2004 BPA Funding Proposal
         Matrix




                                                                                            199101903
                                                                                                            199101904
                                                                                                            24012
                                                                                                                                           24013
                                                                                                                                                    24014
                                                                                                                                                             24018
                                                                                                                                                                             24019
Project Proposal ID




                                                                                                            5              Recom. Action

                                                                                                                                           Recom. Action
                                                                                           High Priority

                                                                                                           High Priority




                                                                                                                                           High Priority

                                                                                                                                                            High Priority

                                                                                                                                                                            High Priority
                                                                                                                                           Priority
Provincial Team Funding Recommendation
Headwaters and Associated Uplands (includes all mountain tributaries)
Objective 1: Reconnect five blocked tributaries over the next three years.                 +
Objective 2: Reduce fine sediments in critical spawning areas in five indexed streams      +
over the next three years.
Objective 3: Restore natural pool frequency to that of undisturbed referenced reaches      +
in five streams over the next three years.
Objective 4: Eradicate or suppress non-native or hybridized populations from five          +
streams over the next three years.
Objective 5: Alter 2,008 acres of forest structure and composition in the South Fork of    +
the Flathead over the next three years, consistent with management and mitigation
plans.
Objective 6: Acquire and/or protect key habitat parcels (endangered, threatened, and                                                                        +
sensitive species habitats) through purchase, conservation easements, or
conservation agreements to assist in maintenance of viable populations.

Impoundments (includes Hungry Horse Reservoir, Flathead Lake, Swan Lake,
and irrigation impoundments)
Objective 1: Reduce negative non-native species interactions in Flathead Lake and          +                                                                                +
three irrigation impoundments over the next three years.
Objective 2: Meet the TMDL goal for reduction in phosphorus.
Objective 3: Reduce the frequency of Hungry Horse refill failure (to within five feet of   +
full pool) as compared to historic operation.
Objective 4: Protect, restore, and enhance riparian/wetland habitat in the upper and                                                                        +
lower Flathead valleys over the next three years, meeting the annual goals set forth in
management and mitigation plans.

Regulated Mainstems (includes South Fork, Upper Flathead, Lower Flathead,
Jocko River)
Objective 1: Move Hungry Horse operations 50 percent closer to normative compared          +
to current operations over the next three years.
Objective 2: Protect, restore, and enhance riparian/wetland habitat in the upper and                                       +                                +
lower Flathead valleys over the next three years, meeting the annual goals set forth in
management and mitigation plans.
Objective 4: Complete an operational impact assessment and develop plans to                                                                +
mitigate for any impacts that the operations of Hungry Horse Dam may cause to the
development and successional trends of riparian wildlife habitats and their associated
aquatic components, in cooperation with ongoing fisheries mitigation activities.
Objective 5: Deal with ongoing recreation-fisheries-water quality conflicts on a daily     +                                                                +
basis, and educate the public to reduce these conflicts.

Unregulated Mainstems (includes North Fork, Middle Fork, and Swan Rivers)
Objective 1: Treat all sites that have occurrences of purple loosestrife or Eurasian
water milfoil.



         Flathead Subbasin Summary                             126                                                                                   3/6/01
                                                                                            199101903
                                                                                                            199101904
                                                                                                            24012
                                                                                                                                           24013
                                                                                                                                                    24014
                                                                                                                                                              24018
                                                                                                                                                                              24019
Project Proposal ID




                                                                                                            5              Recom. Action

                                                                                                                                           Recom. Action
                                                                                           High Priority

                                                                                                           High Priority




                                                                                                                                           High Priority

                                                                                                                                                             High Priority

                                                                                                                                                                             High Priority
                                                                                                                                           Priority
Provincial Team Funding Recommendation
Objective 2: Protect, restore, and enhance riparian/wetland habitat in the upper and                                       +                                 +
lower Flathead valleys over the next three years, meeting the annual goals set forth in
management and mitigation plans.
Objective 3: Deal with ongoing human/wildlife conflicts on a daily basis, and educate                                                                        +
the public to reduce human/wildlife conflicts.

Valley Tributaries & Wetlands (includes all valley tributaries and the Whitefish
and Stillwater rivers)
Objective 1: Eliminate three sources of non-native or hybridized fish populations over     +
the next three years.
Objective 2: Protect, restore, and enhance riparian/wetland habitat in the upper and                                                                         +
lower Flathead valleys over the next three years, meeting the annual goals set forth in
management and mitigation plans.
Objective 3: Significantly reduce the level of sedimentation in five impacted spawning     +                                                                 +
areas over the next three years.
Objective 4: Maintain temperatures within the tolerance range of native fish species.      +                                                                 +
Objective 5: Deal with ongoing human/wildlife conflicts on a daily basis, and educate                                                                        +
the public to reduce human/wildlife conflicts.
Objective 6: Develop a reintroduction plan for Columbian sharp-tailed grouse in the                                                                                          +
Flathead Basin.

Lakes (includes connected and closed-basin lakes)
Objective 1: Remove the sources of non-native or hybridized trout from two to three            +
connected lakes each year over the next three years.
Objective 2: Deal with ongoing human/wildlife conflicts on a daily basis, and educate          +                                                             +
the public to reduce human/wildlife conflicts.
Objective 3: Protect, restore, and enhance riparian/wetland habitat in the upper and                                                                         +
lower Flathead valleys over the next three years, meeting the annual goals set forth in
management and mitigation plans.
Objective 4: Maintain the trophic status of all classified lakes.                              +                                                                             +
Objective 5: Increase the angler opportunities in three closed-basin lakes over the            + +
next three years.
These project titles are referenced by ID above:
199101901- Hungry Horse Mitigation – MFWP
199101904- Stocking of Offsite Waters for Hungry Horse Mitigation – Creston National Fish Hatchery - USFWS
24012 – Riparian Habitat Preservation – Weaver Slough & McWinegar Slough - FLT
24013 – Assessment of Operational Impacts of Hungry Horse Dam on Riparian Wildlife Habitats and Their Associated                                            Aquatic
Components – MFWP
24014 - Assessment of Operational Impacts of Libby Dam on Riparian Wildlife Habitats and Their Associated                                                   Aquatic
Components – MFWP
24018 – Secure and Restore Critical Fish and Wildlife Habitat – CSKT
24019 – Research, Monitor and Restore Native Species - CSKT

        Note: + = potential or anticipated effect on subbasin objectives and strategies.


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        Flathead Subbasin Summary                             127                                                                                    3/6/01

				
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