Compilation of Information on
Coho Salmon and Steelhead Trout
Collected Between 1994-2003
in the Tomales Bay Watershed with
Recommendations for Future Actions
A List of Partners and Selection Criteria
for Future Salmonid Restoration Projects
Marin County, California
Neysa King, Watershed Coordinator
Tomales Bay Watershed Council
P.O. Box 447 Point Reyes Station, California 94956
Funding provided by the California Department of Fish and Game,
Salmon and Steelhead Trout Restoration Account
Table of Contents
ANNOTATED BIBLIOGRAPHY OF SALMONID REFERENCES 1994-2003
AND RECOMMENDATIONS FOR FUTURE ACTIONS
I. Introduction…………………………………………………………………… 3
II. Tomales Bay Watershed Description………………………………………… 3
A. Climate…………………………………………………………………… 6
B. Geology and Erosion…………………………………………………….. 6
III. Annotated Bibliography of Literature and Information Collected in the
Tomales Bay Watershed Between 1994-2003 on Salmonid Populations
and Habitat Assessments…………………………………………………….. 7
A. Tomales Bay Watershed Databases and Reports………………………... 8
B. Lagunitas/Olema Creek Sub-Watershed………………………………… 17
C. Walker Creek Sub-Watershed…………………………………………… 25
D. Historical Salmonid Planting in the Tomales Bay Watershed…………... 26
E. Summary………………………………………………………………… 27
F. Recommendations ………………………………………………………. 28
Figure 1. Map of the Tomales Bay Watershed………………………………..…… 4
Table 1. Coho Salmon Spawning Survey Data for Overall Lagunitas Creek
Table 2. Summary of Walker Creek Salmonid Planting 1970-1980……………… 27
References cited……………………………………………………………………… 35
Annotated references………………………………………………………………… 36
LIST OF PARTNERS AND SELECTION CRITERIA
FOR FUTURE RESTORATION PROJECTS
I. Organizations and Agencies Participating in Salmonid Restoration and
Assessment Activities in the Tomales Bay Watershed……………………… 31
Appendix A: Draft Salmonid Restoration Project Ranking Criteria for Use in
the Tomales Bay Watershed…………….…………………………………………... 38
Appendix B: Lagunitas Creek Watershed Coho Salmon Planting History…………. 45
Appendix C: Comprehensive List of Salmonid and Related Aquatic References for
the Tomales Bay Watershed…………………………………………………………. 47
1994-2003 ANNOTATED BIBLIOGRAPHY OF
SALMONID INFORMATION AND RECOMMENDATIONS FOR FUTURE ACTIONS
The Tomales Bay watershed is remarkable for its beauty, wildlife, and diverse human history.
Tomales Bay is created by the San Andreas Fault and underlying geology, resulting in a striking
contrast between the oak woodland and open grasslands to the east of the Fault, with dark and
thick conifer and hardwood forests to the west. For both human and non-human communities
that live here, and for others that migrate through, Tomales Bay and the surrounding watershed is
The Tomales Bay watershed includes a broad diversity of both aquatic and terrestrial habitats.
This abundance of plant and animal life depends on habitats in the bay and surrounding
watershed for shelter, foraging, nesting and rearing needs. Nearly 900 species of plants, 490
species of birds, hundreds of invertebrate species, and many other species including, numerous
sensitive, threatened and endangered species inhabit the watershed and nearby Point Reyes
peninsula. Sensitive species include federally listed species such as coho salmon, steelhead
trout, brown pelican, Steller sea lion and red-legged frog. Other sensitive species that have state
or local significance include tule elk, Point Reyes jumping mouse, and river otter, and numerous
endemic and rare plants.
The local populations of coho and steelhead salmon depend on the many tributary streams that
flow to Tomales Bay, and on the Bay itself. Notably, Lagunitas Creek watershed is considered
to be one of the most important creek basins for remnant wild coho in the Central California
Evolutionarily Significant Unit (ESU). Current estimates of the coho population in this creek are
that approximately 500 adults return to the system each year to spawn, and this run is one of the
most robust left in the state albeit one in danger of extirpation in the near future (PRNS 2001).
During the last century, salmonid habitat in the Tomales Bay watershed has been diminished to
less than half of the original range by the construction of reservoirs and roads, and remaining
habitat has been compromised by other human activities. In addition to Lagunitas Creek, Olema
Creek and numerous other tributaries to this system support both coho and steelhead, and Walker
Creek watershed and some of the small streams that flow directly to Tomales Bay continue to
provide spawning and rearing habitat for steelhead each year.
II. Tomales Bay Watershed Description
The Tomales Bay watershed comprises an area of approximately 220 square miles and has two
main tributaries, Walker and Lagunitas creeks (State of California Department of Health
Services, 2002). The catchment area for Tomales Bay is a rural watershed of mostly pastureland
and parklands with low human population density. The Tomales Bay watershed is mostly
comprised of two sub-watersheds formed by Walker and Lagunitas creeks and their tributaries
Figure 1. The Tomales Bay watershed (map courtesy Point Reyes National Seashore).
Elevation in the 76-square mile Walker Creek sub-watershed ranges from 1,500 feet to sea
level, where the creek empties into Tomales Bay just south of its mouth. The northern tributaries,
Keyes Creek and Chileno Creek, flow through wide valleys with gentle, grassy hills. The upper
watershed is much more rugged with extensive areas of coast live oak forest. Soils, underlain by
Franciscan formation sandstone and shale, are highly erodible (Kashiwagi, 1985). This sub-
watershed contains a 220-acre natural lake, Laguna Lake, at the top of Chileno Valley. Soulajule
Reservoir, constructed in 1968 in Arroyo Sausal and enlarged in 1980, is managed by the Marin
Municipal Water District. Over 95% of the watershed is in private ownership (Prunuske
Chatham, Inc. 2001). Since European settlement, land use in the Walker Creek watershed has
been mostly agricultural. Riparian habitat has been diminished, and marshes such as an
extensive one in upper Arroyo Sausal, where the cheese factory is today, have been drained. The
only concentrated development in the Walker Creek watershed occurs in the small town of
The Lagunitas Creek watershed is the largest drainage to Tomales Bay with an area of 103-
square miles. Rainfall in the upper watershed averages 50 inches per year, compared to 25-inches
in Chileno Valley. Halleck Creek, Nicasio Creek, San Geronimo Creek, and mainstem Lagunitas
Creek through Samuel P. Taylor State Park have areas of dense redwood growth and cool water
year round. Except for a few open areas, most of Lagunitas Creek downstream of the state park
is thickly forested with willows and alders. Lagunitas Creek is fed by six main tributaries:
Olema, Nicasio, San Geronimo, Bear Valley, Devil’s Gulch and Deadman’s Gulch creeks
(Niemi and Hall, 1996). Cheda Creek is another tributary of note downstream of Devil’s Gulch.
Much of the streamflow in mainstem Lagunitas Creek is regulated by dams and collected into
various reservoirs upstream of the San Geronimo confluence, with Olema and San Geronimo
creeks being the largest uncontrolled tributaries -- neither has a dam or reservoir on the
mainstem. Olema Creek flows for nine miles along the San Andreas Fault Zone, with a
catchment area of 14.5 square miles (PRNS, 2001b). Olema Creek and tributaries provide
significant fisheries and aquatic habitat. Over half of the watershed is in public ownership.
Ranching -- on both private lands and on land leased from the National Park Service (NPS) --
continues in the Olema and Nicasio valleys, and in the lower Lagunitas valley. The Lagunitas
Creek watershed also contains many small communities, namely: Woodacre, San Geronimo,
Forest Knolls, and Lagunitas in San Geronimo Valley, Nicasio, Olema, and Point Reyes Station.
The upper part of the watershed is owned and managed by MMWD for water supply to east
Marin County. MMWD has five reservoirs in the watershed - four on mainstem Lagunitas Creek,
and Nicasio Reservoir on Nicasio Creek.
There are a number of small, steep streams on the east and west shores that flow directly into
Tomales Bay. These small streams drain approximately 30 square miles of the Tomales Bay
watershed. On the eastern shores, these streams include Tomasini Canyon and Millerton Creek
among various others. Western shore streams include Haggerty Gulch, Trout Hatchery Creek,
Redwood Creek, and First, Second and Third Valley creeks in Inverness.
Tomales Bay proper is a 28 km2 shallow, highly unidirectional, Mediterranean-type, coastal
estuary. Tomales Bay opens at the southern end of Bodega Bay and extends in a southeasterly
direction. The bay is approximately 12 miles long and less than one mile wide (State of
California Department of Health Services, 2002). The bay alternates between a classical estuary
(net dilutive basin) during wet winter months, and a hypersaline estuary (net evaporative basin)
during dry summer months. The average depth of the bay is less than 20 feet (State of California
Department of Health Services, 2002).
Tomales Bay hosts a diversity of habitats including, intertidal, subtidal, benthic, mud flats, and
salt and freshwater marshes. Also of note are the Tomales Bay dunes, which have a profound
effect on tidal circulation and water depth at the mouth of the Bay. Large subtidal meadows of
eelgrass grow in the northern half of Tomales Bay, between Pelican Point and Tom’s Point,
where temperatures and salinities reflect those in the Pacific Ocean. This outer region of the bay
is influenced by nutrients and plankton brought in by the tide from the ocean, as well as by the
freshwater inflow and nutrients from Walker Creek (Smith and Hollibaugh, 1997).
The Tomales Bay watershed has a Mediterranean climate consisting of mild dry summers and
cool wet winters. The climate is highly variable in this typical coastal region of California. The
basin-wide average rainfall is over 30 inches per year with a range between 20 to 61 inches.
Ninety percent of the rainfall occurs between the months of October and April. Fog is most
prevalent along the coast during the hottest summer months – July through September - and may
cover the landscape for 50 miles inland.
B. Geology and Erosion
As described by Wahrhaftig & Wagner (1972), there are various erosional processes that affect
the landscape of the Tomales Bay watershed. On the slopes of hills, these include: sheetwash
and rainwash of bare soil; piping or the erosion of sediment by storm waters moving through
cracks in the soil; rilling and gullying; landslides; debris flows; and the slow down-hill
movement of a thin piece of soil mantle. This material eventually moves into the streams and is
carried as bedload (gravel and sand) or as suspended sediment (fine sand, silt and clay),
ultimately ending up in Tomales Bay or the ocean.
The Walker Creek basin lies adjacent to the San Andreas Rift Zone. Its moderate relief is
underlain by the highly unstable Cretaceous Franciscan Formation mélange. Stream bank
erosion is a particular problem in streams that lack riparian vegetation (UCCE, 1995). Because
eroded material is deposited directly into streams and the bay it is a primary source of water
quality and habitat degradation. A combination of intensive farming in the late 1800s to early
1900s and large storm events have contributed to erosion in the upper watershed, destabilizing
downstream channel banks and covering salmonid rearing habitat. Along the mainstem of
Walker Creek and Chileno Creek watersheds stratified layers of sand, gravel, stones, and cobble
that were deposited by water characterize the soil. Soils along the Keyes Creek channel consist
of deep, poorly drained silt and clay loams. Salmon Creek and Arroyo Sausal soils consist of
gravelly sandy loam, deep and well-drained with rapid permeability.
The Lagunitas Creek basin is underlain primarily by Franciscan formation composed of
graywackes, sandstones, shales, greenstones, and serpentines (Hecht, 1983). The greenstones
that underlay the channel in the stretch that runs through Samuel P. Taylor State Park are a
source of clear water and the boulders and cobbles that weather from the greenstone provide
suitable spawning habitat (UCCE 1995). The geology and topography of Olema Creek
watershed are more determined by the San Andreas Fault, as it is a linear drainage that flows
along the fault rift zone.
For background information on water quality, soils, erosion, sedimentation and other watershed
characteristics as well as the human history and uses of natural resources, please see the Tomales
Bay Watershed Stewardship Plan: A Framework for Action (TBWC, 2003). This plan
summarizes literature about Tomales Bay, its tributaries and the watershed; including past
reports, studies and assessments to evaluate aquatic habitats, sedimentation and geomorphology,
and sub-watershed restoration plans.
III. Annotated Bibliography of Literature and Information Collected in
the Tomales Bay Watershed Between 1994-2003 on Salmonid
Populations and Habitat Assessments
The following annotated bibliography is intended to facilitate easy access to recent population
and habitat information on coho and steelhead collected in the Tomales Bay watershed between
1994-2003. Only information sources that were completed and/or published during this period
are included here. Please do not cite these as primary literature sources as the information
presented has been excerpted out of documents whose entirety warrants review.
During these last 10 years, different types of population and habitat data have been collected, but
little effort has been made to standardize, compare or analyze the data or correlate results of
different studies. None of the conclusions presented here have been evaluated or altered from
their original form as presented in the source documents. Additionally, there are sometimes
conflicting data, conclusions and/or recommendations, and many studies lack peer review,
further emphasizing the need for a comprehensive synthesis and analysis of salmonid
information in the Tomales Bay watershed. Such a synthesis will increase our understanding of
the current status, trends and needs of these important species.
This report includes only information collected in the Tomales Bay watershed, and does not
address the link between oceanic influences and local salmonid populations. In 2004, a Limiting
Factors Analysis of the Lagunitas/Olema Creek sub-watershed will be initiated by the Marin
Resource Conservation District with assistance from the Lagunitas Advisory Group (LAG)
which includes representative from the Tomales Bay Watershed Council -- Point Reyes National
Seashore, Marin Municipal Water District, Salmon Protection and Watershed Network, Regional
Water Quality Control Board, California Department of Fish and Game -- and others as part of
the Lagunitas Creek Watershed Improvement Program (funded by the State Water Resources
Control Board’s Proposition 13 Grant Program).
The Lagunitas Creek Watershed Improvement Program is a three-year project that includes
watershed restoration projects intended to reduce sediment inputs and restore critical watershed
processes. A Limiting Factors Assessment will be used to identify restoration actions that will
promote recovery of coho, steelhead, and shrimp populations, and to refine water quality (Total
Maximum Daily Load) problem statements. The general status of other important indicator
species and aquatic ecosystem health will be qualitatively incorporated into this assessment.
The overall purpose of the Limiting Factors Assessment (LFA) is to fill information gaps related
to physical and biological factors controlling salmonid and shrimp population dynamics within
an ecosystem context in the Lagunitas/Olema sub-watershed. More specifically, the LFA will
include a salmonid and aquatic wildlife population dynamics study that will focus on factors
limiting1 coho salmon, steelhead trout, and California freshwater shrimp populations in the
unregulated2 portions of the Lagunitas Creek watershed including San Geronimo Creek,
Lagunitas Creek mainstem, Devils Gulch, and Olema Creek. While this study will focus on these
endangered species, it will be conducted within an aquatic community ecological framework that
can be used to answer questions related to a broad spectrum of aquatic species and indicate the
overall health of the aquatic ecosystem. A technical subcommittee advises the LAG on technical
issues related to the program’s scientific studies.
During 2004-2005, the Point Reyes National Seashore, through their Coho Salmon and Steelhead
Trout Restoration Project, will also synthesize and analyze salmonid data to provide information
about fisheries needs in portions of the Lagunitas/Olema sub-watershed. Additional on-going
studies include the development of a Tomales Bay hydrodynamic model (University of
California Berkeley), Codar monitoring of off-shore currents (Paul Siri), and modeling to
evaluate links between the Lagunitas/Olema sub-watershed, Tomales Bay and the Pacific Ocean
as part of the Lagunitas Creek Limiting Factors Study. A comprehensive list of salmonid and
related aquatic references for the Tomales Bay watershed is included in Appendix C. This initial
effort to identify all of the primary information sources was not confined to the period from
1994-2003, and it may have overlooked some of the less accessible sources of information (e.g.
unpublished field notes, memos, etc.).
A. Tomales Bay Watershed Databases and Reports
In 2003, the California Department of Fish and Game (CDFG), with the assistance of recovery
teams representing diverse interest and perspectives, created the Recovery Strategy for
California Coho Salmon (Oncorynchus kisutch) (recovery strategy). This recovery strategy
will guide CDFG in their efforts to recover coho salmon on the north and central coast of
California. The recovery strategy uses the best science available to CDFG to initiate some
actions and projects that can commence immediately, and makes recommendations for medium
and long-term tasks. The recovery strategy is organized at two scaled. The first is a broad
Limiting factors refer to physical or biological factors which constrain biological populations and prevent population increase
over a certain level. A limiting factors analysis integrates life history features with habitat requirements and environmental
conditions encountered by the species of interest. For coho salmon and steelhead, key life history stages include: upstream
migration, spawning and incubation, fry rearing, juvenile rearing (summer and winter), and outmigration. When habitat is in
short supply or very poor in quality at any life stage, mortality may be so high that population levels cannot increase. Such
habitat attribute(s) are referred to as limiting factors. Identification of limiting factors is an important element in determining
Unregulated, in this context, refers to those streams and portions of streams below reservoirs in the Lagunitas Creek watershed;
including the mainstem of Lagunitas Creek below Kent Lake and Nicasio Reservoir.
geographic, range-wide resolution, while the second level is at a finer scale that identifies actions
within specific watersheds. The recovery strategy emphasizes cooperation and collaboration at
many levels including public and private support for restoration actions, funding, and achieving a
balance between regulatory and voluntary efforts. The recovery strategy identifies goals and an
implementation plan, as well as cost projections for these tasks. Locally specific
recommendations include the following:
Lagunitas Creek Sub-Watershed
• Use recommendations of exiting sediment source surveys to restore habitat of coho
salmon. Augment surveys as necessary. Expand inventories as needed for a
comprehensive watershed approach for coho salmon passage.
• Coordinate with appropriate agencies to restore coho salmon passage at barriers
identified by Ross Taylor, SPAWN, and others. Complete any needed surveys of
• Investigate opportunities for restoring historic runs of coho salmon.
• Encourage the MMWD to commit ongoing resources and support of stewardship in the
basin beyond the ten-year mitigation order that expires in 2007 to include: riparian
enhancement and protection, sediment source reduction, habitat typing and surveying,
coho salmon surveys and counts, water conservation, outreach and education,
effectiveness monitoring of projects, planning and assessment of potential restoration
projects to benefit coho salmon.
• Provide incentives for septic inspection, repair, and replacement to reduce aquatic
• Assess, evaluate, and implement habitat restoration actions in Nicasio Creek.
• Develop a monitoring and assessment program for the estuarine reaches of Lagunitas
Creek and inter-tidal reaches of Tomales Bay, looking at impacts to coho salmon rearing
• Consider restoration of Olema Marsh, Bear Valley Creek, and the mouth of Olema Creek,
to benefit coho. The restoration should provide rearing habitat refuge during high flows,
habitat protection, and food production. Hydrologic connectivity between marshes
should be restored.
• Throughout the Lagunitas Creek drainage, work with private landowners to encourage
biotechnical bank stabilization, riparian protections, woody debris retention, and timing
of water withdrawals to help protect coho salmon.
• In the San Geronimo Creek sub-watershed, continue public outreach and education for
private landowners, residents, commercial, public utility and county works regarding best
management practices to control erosion, protect riparian vegetation, retain LWD, and
minimize disturbance to coho salmon from pets.
• In the San Geronimo Creek sub-watershed, encourage removal of non-native fish species
from stock ponds where they are a threat to coho salmon.
• In the San Geronimo Creek sub-watershed, Marin County should determine a policy for
reviewing new development projects and impacts to the creek from new well
construction. The County should consider adopting recommendations for well
developments from the Local Coastal Plan.
• Encourage the National Park Service to continue practices to benefit coho salmon,
including restoration projects, sediment control projects, locating well constructed fences
out of riparian zones, repairing headcut gullies as possible, and implementing rotational
grazing in locations to minimize erosion and impacts to the creek.
• Encourage the Marin Municipal Water District and County of Marin to continue to
implement and coordinate their Watershed Protection Agreement Program for additional
water hook-ups in Nicasio and San Geronimo Creek watersheds.
• Look for opportunities to restore natural channel form and function in the upper
watershed to protect summer flows into San Geronimo Creek.
• Encourage continuation of riparian protection and sediment control projects. Focus on
working with landowners to mange livestock to protect riparian areas, and to implement
erosion control projects on state and federal parkland and on private lands (e.g. Devil’s
• Continue public outreach and education for private landowners, residents, commercial,
public utility and county workers regarding best management practices to control erosion,
protect riparian vegetation, retain LWD, and minimize disturbance to coho salmon from
Walker Creek Sub-Watershed
• Continue to fund and support landowners and the Marin RCD to restore riparian zones
and manage livestock to increase stream protection and soil retention. Address water
quality and nutrient loading issues by encouraging sustainable land management
practices, controlling sediment sources, protecting riparian zones and employing BMPs
that encourage permeability and infiltration.
• Continue to support active watershed groups, encouraging a focus on coho salmon
restoration where appropriate.
• Assess the water temperature regime during the summer season for three to five years to
determine the role of water temperature as a limiting factor in coho salmon production.
• Support landowners and the Marin RCD in projects to improve channel conditions and
restore natural channel geomorphology, including side channels and dense contiguous
• Implement high priority fishery enhancement projects for the reduction of sediment
delivery and the restoration of riparian corridors as listed in the Walker Creek
Enhancement Plan (2001).
• Look for opportunities to increase woody debris retention and recruitment.
• Encourage the MMWD to continue to assess the release of water from Soulajule
Reservoir to develop the optimum release for coho salmon.
• Support a coho salmon limiting factors assessment in Keyes Estero and Tomales Bay.
The most comprehensive electronic archive of salmonid, water quality, aquatic habitat and
general watershed information currently available for the Tomales Bay watershed is presented in
the Draft KRIS West Marin-Sonoma Database (2003) recently completed by the Institute for
Fisheries Resources (IFR). This database has compiled reports and information that were
accessible during a two-year literature collection that included information from public agencies,
local organizations and other participating individuals. The information is electronically
- 10 -
available and presented in summary graphs and maps, with links to the metadata. The following
are examples of the type of information that are available in this database:
Lagunitas Creek watershed
• One chart shows the number of juvenile coho per 30-meter reach of stream provided by
the Marin Municipal Water District (MMWD) for the Lagunitas Creek watershed for
some years from 1970-2000. Surveys in 1970, 1980, 1982-1988, and 1990 were
conducted by the California Department of Fish and Game and separate topics provide
more data on these surveys. The more recent data were collected by MMWD or their
contractors and the National Park Service. No surveys of this kind were conducted in
1971-79, 1981, 1989, 1991, and 1992.
• Another chart reflects the number of salmonid juveniles per 30 meters of stream habitat
based on electrofishing of index reaches in Devils Gulch from 1993-2000. These data
were collected by Marin Municipal Water District staff (1997-2000) and their contractors
Trihey and Associates (1994-1996), and Sierra Fisheries (1993).
Walker Creek watershed
• On October 12, 2001, the California Department of Fish and Game surveyed two reaches
(ten pools each) in Walker Creek to look for coho salmon. Steelhead was the dominant
species in both samples but coho were not found in either reach. The KRIS database
further states that although coho were absent in samples, it cannot be inferred that they
were totally absent from Walker Creek as they may be present in other years or at low
levels in other reaches of the stream. CDFG had previously electro-sampled Walker
Creek in 1981 looking for coho, and found none.
• Another graph shows the number of erosion sites at each priority level in the sub-
watersheds of Walker Creek. These data were produced as part of an erosion inventory
conducted by Prunuske Chatham Inc. for the Marin Resource Conservation District in
2001. The survey identified 196 sites throughout the Walker Creek watershed,
downstream of Soulajule Dam and Laguna Lake, where private landowners granted
permission. Therefore, note that figures do not represent all erosion sites within the
watershed, but those where investigation occurred.
In December 2003, the NOAA Southwest Fisheries Science Center, Santa Cruz Laboratory
published the Report on the Genetics of Coho Salmon (Oncorhynchus kisutch) held at Warm
Springs (Don Clausen) Hatchery for Recovery Efforts in the Russian River. This report
reviews the current status of the Russian River coho population, and evaluates the genetics of
nearby populations for an ex situ recovery program (namely, the Lagunitas/Olema Creek coho
population). The on-going multi-year recover program involves the capture and rearing of
juvenile fish that are found in areas that are at high risk of drying up. The intention is to breed
them at reproductive maturity at the Warm Springs Hatchery, and to release the offspring into
Russian River tributaries that are currently unoccupied by the species.
- 11 -
According to the report, at the time of program initiation very little was known about the
genetics of coho salmon in California. The Santa Cruz Laboratory evaluated genetic variability
and compatibility within and between populations of coho. The Lagunitas/Olema Creek
watershed was determined to harbor the most geographically proximate, persistent, population of
coho salmon and is a good a priori donor candidate, should such supplementation be deemed
In July of 2002, tissue samples from the 308 fish being held at Warm Springs Hatchery were
transferred to the Santa Cruz Laboratory (SCL) for genetic analysis. This includes fish from
three tributaries of the Russian River as well as fish from Lagunitas/Olema Creeks. All fish were
captured in the summer of 2001 as juveniles and should become reproductively mature in the
winter of 2003-04.
In their conclusions and recommendations, the study finds that their data indicate that the
Russian River and Lagunitas/Olema Creek populations of coho salmon constitute two separate
populations, with little or no contemporary gene flow between them. Because at least some of
the differences between these stocks are likely involved in local adaptation, interbreeding the two
stocks could cause significant outbreeding depression and is not recommended. However, fish
from the 3 tributaries of the Russian River in the 2001 year class can be treated as one population
and interbred. The study also evaluated the potential for, and strategies to avoid, inbreeding and
inbreeding depression which can also run the risk of decreasing offspring fitness.
The genetic findings of this study led to a set of broad options for what to do with the
Lagunitas/Olema Creek fish that were being held at the Warm Springs Hatchery, which were not
to be released to the Russian River system. After discussing the different options for release
and/or letting the fish die at the hatchery, the final recommendation was to release these coho to
a stream that does not have a population of coho. The final recommendation in this report is to
release the coho into the Walker Creek watershed for geographic, genetic and political reasons.
They conclude that this release may establish a satellite population which is an important safety
element to the current Lagunitas/Olema Creek population, and would pose relatively low risks
when considering genetic and disease related factors of hatchery-reared fish.
The Tomales Bay Watershed Stewardship Plan: A Framework for Action (July 2003) presents
a summary of the existing literature about the bay and its watershed; including, human uses of
natural resources, water quality and sedimentation. The Plan also includes a set of watershed
stewardship goals and an action plan for implementation, with prioritized recommendations for
future efforts. The Plan has been endorsed by 25 local watershed stakeholder organizations
which include federal, state and local agencies; local environmental organizations; agricultural
and maricultural groups; local business and village associations.
The Council will continue its efforts in the future to foster needed action to restore and protect
aquatic and terrestrial habitats in the Bay and watershed, to improve water quality, and to
oversee implementation of needed programs and projects that are prioritized in the Plan. To
- 12 -
promote effective project selection and implementation in the watershed, the Council has
developed a matrix for Salmonid Restoration Project Ranking Criteria for use in the Tomales
Bay watershed (see Appendix A). By working cooperatively to select the best projects with the
highest likelihood of success, the Council hopes to improve our collective efforts to improve
both coho and steelhead populations and their habitats.
The Plan includes the following priorities for salmonid habitat restoration and assessment.
• Restore salmonid habitat and remove barriers to migration. Assess condition of
salmonid and freshwater shrimp habitats. Specifically, identify limiting factors for
salmonids and freshwater shrimp populations in Lagunitas Creek and analyze the
limiting factors for salmonids in Walker Creek and other tributaries with historic
• Help landowners to protect and enhance riparian and wetland habitats. Promote and
assist in coordination of all types of voluntary restoration efforts and projects.
• Provide incentives and support for habitat protection and enhancement.
• Assure that regulated water releases by agencies and other entities with
impoundments in the watershed are sufficient to sustain downstream coldwater
• Assess current water flow conditions and develop a plan to increase water flows if
necessary to restore key habitats.
• Ensure optimal streamflow to sustain native aquatic communities through water
conservation and range management where feasible.
• Ensure optimal streamflow patterns to sustain native aquatic communities by limiting
the impacts of development (e.g. residential, commercial, public works and water)
• Support funding for wetland protection and conservation easements on public and
In June 2003, the Marin County Stream Crossing Inventory and Fish Passage Evaluation was
completed by Ross Taylor and Associates for the County of Marin, Department of Public Works.
This report presented an inventory and fish passage evaluation of county-maintained stream
crossings within the County of Marin that was conducted between May 2002 and June 2003.
The primary objective was to assess passage of juvenile and adult salmonids and to develop a
project-scheduling document to prioritize corrective treatments to provide unimpeded fish
passage at road/stream intersections. The inventory was focused primarily on County-
maintained crossings with anadromous stream reaches within Marin County watersheds known
to historically and/or currently support runs of coho salmon and/or steelhead. However, a
number of city and state-maintained crossings were also evaluated.
The final report includes the following for each of the 90 stream crossings that were evaluated,
which is also compiled in spreadsheet form for database development:
• A county and location of all stream crossings with culverts, including stream name, road
name, mile marker, coordinates, etc.
- 13 -
• For each site, culvert specifications were collected.
• Information regarding culvert age, wear, and performance was collected.
• An evaluation of fish passage at each culver location using two methods. Using the first
method, fish passage was assessed by employing a first-phase evaluation filter that was
developed for Part 10 of the CDFG Salmonid Stream Habitat Restoration Manual to
determine if a culvert met fish passage criteria for all species and life stages as defined by
CDFG for the range of migration flows completely, partially or if it failed. Then,
FishXing (a computer software program) was used to conduct in-depth passage
evaluations for the sites with a “partial” score in the initial screening.
• Digital photo documentation of each crossing was taken to provide visual information
regarding inlet/outlet configurations, as well as for use in future reports, proposals, etc.
• An evaluation of the quantity and quality of fish habitat above and below each crossing
location. Most information was obtained from habitat typing and fisheries surveys
previously conducted by various federal and state agencies, as well as watershed groups
and private consultants. Where feasible, first-hand inspection and evaluation of stream
• A ranked list of culverts that require treatment to provide unimpeded fish passage to
spawning and rearing habitat. On a site-by-site basis, general recommendations for
providing unimpeded fish passage were provided.
According to this report, the top 10 migration barriers (in order from highest to lowest) on creeks
within the Tomales Bay watershed which are thought to support both coho and steelhead that are
prioritized for restoration action: John West Fork (Blue Line Creek), tributary to Olema Creek at
Highway 1; Giacomini Gulch, tributary to Olema Creek at Highway 1; West Fork Woodacre
Creek, tributary to Lagunitas Creek at Redwood Drive; Woodacre Creek, tributary to Lagunitas
Creek at San Geronimo Valley Rd.; Woodacre Creek, tributary to Lagunitas Creek at Park Street;
Bates Canyon, tributary to Lagunitas Creek at San Geronimo Valley Rd.; San Geronimo Creek,
tributary to Lagunitas Creek at Railroad Ave.; Old Bear Valley Creek, tributary to Lagunitas
Creek at Sir Francis Drake Blvd.; Woodacre Creek, tributary to Lagunitas Creek at Carson Rd.;
and Cheda Creek, tributary to Olema Creek at Sir Francis Drake Blvd.
In April 2001, the Southwest Fisheries Science Center (Santa Cruz Laboratory) published a
Status Review Update for Coho Salmon (Oncorhynchus kisutch) from the Central California
Coast and the California portion of the Southern Oregon/Northern California Coasts
Evolutionarily Significant Units. In this report, presence-absence data and population trend data
were analyzed. Overall, the percentage of sampled streams for which coho salmon were found
to be present declined over the 1989-2000 time period, with greater declines occurring in the
southern part of the range. In the Central California Coast ESU, coho historical presence was
identified in 278 streams, 16 of which are in Marin County.
In this report, historical population information for adult coho spawner surveys in Lagunitas
Creek and its tributaries dated back to the 1950’s. Early surveys from 1950-1970 were
conducted by the California Department of Fish and Game. Although these surveys document
- 14 -
distribution and could provide a coarse index of abundance in certain reaches, they are not robust
enough to be used in a more detailed assessment of population trends. A more consistent record
of redd counts in Lagunitas Creek and three of its tributaries (Olema and San Geronimo creeks,
and Devil’s Gulch) is available from 1995-2000 (see above MMWD 2001 report). The number
of redds in these streams has remained fairly constant over the past six years, with the highest
accounts occurring in the 1996-97, 1997-98, and 1999-2000 spawning seasons. No historical
datasets with six or more years of record were available for smolts, nor were there historical
datasets for juveniles. Data on summer juvenile abundance is available however for Lagunitas
Creek and two of its tributaries for 1993-2000. These data for both the 1994 and 1997 brood
years were relatively strong in Lagunitas Creek and its tributaries; however, the overall trend
suggests a decline in abundance. The average abundances (all streams combined) are lower for
1998, 1999, and 2000 than in any of the five preceding years.
The final conclusions of this report state that the Central California Coast ESU is presently in
danger of extinction. The condition of coho salmon populations in this ESU is worse than
indicated by previous reviews, and the California portion of the Southern Oregon/Northern
California Coasts ESU is likely to become endangered in the foreseeable future.
In 1995, the National Marine Fisheries Service completed a Status Review of Coho Salmon
from Washington, Oregon, and California. In October 1993, in response to three petitions
seeking protection for coho salmon under the ESA, NMFS initiated a status review of coho
salmon in Washington, Oregon, and California, and formed a Biological Review Team (BRT) to
conduct the review. This report summarizes biological and environmental information gathered
in that process.
The BRT examined genetic, life history, biogeographic, geologic, and environmental information
to identify where ESU boundaries should be located. In particular, physical environment and
ocean conditions/upwelling patterns, estuarine and freshwater fish distributions, and coho salmon
river entry and spawn timing and marine coded-wire-tag recovery patterns were found to be the
most informative for this process. Based on this examination, the BRT identified six coho
salmon ESUs in Washington, Oregon, and California. The geographic boundaries the Central
California coast, of which Tomales Bay watershed is a part, extend from Punta Gorda in northern
California south to and including the San Lorenzo River in central California, and include
tributaries to San Francisco Bay, excluding the Sacramento-San Joaquin River system.
In this review, the BRT did not evaluate likely or possible effects of conservation measures and,
therefore, did not make recommendations as to whether identified ESUs should be listed as
threatened or endangered species; rather, the BRT drew scientific conclusions about the risk of
extinction faced by identified ESUs under the assumption that present conditions will continue.
The resulting conclusions for the Central California coast ESU was that there was unanimous
agreement among the BRT that natural populations of coho salmon in this ESU are presently in
danger of extinction. The chief reasons for this assessment were extremely low current
abundance, especially compared to historical abundance, widespread local extinctions, clear
- 15 -
downward trends in abundance, extensive habitat degradation and associated decreased carrying
capacity, and a long history of artificial propagation with the use of non-native stocks. In
addition, recent droughts and current ocean conditions may have further reduced run sizes.
The Marin Coastal Watershed Enhancement Project (November 1995), was published by the
University of California Cooperative Extension in response to an increased focus on nonpoint
source pollution by regulatory agencies. The goal of the project was to develop solutions to
water quality and natural resource problems. As such, the report summarizes information on the
status of natural resources and water quality in the project area, reasons for water quality
problems, and steps that can be taken to make improvements. The project area included the
watersheds of Walker and Lagunitas creeks, and smaller tributaries that flow directly into
Tomales Bay from the east shore, and considered many of the agricultural issues within this 232
square mile area.
In general, the report states that in the Walker Creek watershed, stream condition and fish habitat
are severely degraded in many areas, characterized by streambank erosion, lack of riparian
vegetation, lack of cover and woody debris in the channel, high summer water temperatures and
sediment-embedded spawning gravels. Sedimentation has clearly had a devastating effect on
fish habitat in Walker Creek. Many of the deep, cool pools and gravel that salmonids depend on
for spawning and rearing young have been filled in with fine sediment. Because of
sedimentation, the channel has become wider and shallower and water temperature has
increased; tree canopies are not able to shade the wider stream as effectively, and shallower
water heats up more easily.
According to their discussion on salmonids, local residents observed good runs of salmonids
until the late 1970s, when a serious and prolonged drought occurred. Additionally, construction
of Soulajule Reservoir is thought by some locals to be the cause of declining fish populations.
According to this report, observations made during field surveys point toward numerous
contributing factors. MMWD has commissioned many studies since the 1970s to evaluate the
impacts of Soulajule Reservoir, and the Marin Resource Conservation District has worked in
partnership with the University of California Cooperative Extension, Natural Resource
Conservation Service, the County of Marin, and willing private landowners to assess riparian
communities, and a geomorphic assessment is planned for Walker Creek in the near future.
This report found that little quantitative information exists on the present status of salmon and
steelhead runs in Walker Creek, and informal surveys have been conducted by several fisheries
biologists to evaluate habitat condition in this watershed although the inroma6tion is inconsistent
and not always scientifically based. In 1981, the California Department of Fish and Game
conducted an electrofishing survey in Walker Creek and found 5 young of the year coho salmon.
Since 1980, summer flows have been augmented by releases from Soulajule Reservoir.
According to this report, these flows, as well as recommended habitat enhancement measures
over the last decade have not corrected the decline in fish runs and significant sediment sources
remain. Additionally, little is known about water quality throughout most of the watershed.
- 16 -
Large amounts of sediment can be observed in the creek for many days following rainstorms,
and lack of riparian cover on much of mainstem Walker Creek and its tributaries indicates that
high water temperatures are a likely problem.
The report further states that the majority of the Lagunitas Creek watershed is protected as open
space and owned by the Marin Municipal Water District, California State Parks and the Point
Reyes National Seashore/Golden Gate National Recreation Area. There are numerous small
communities within the watershed, with the highest concentration in the San Geronimo Valley.
Similar to the Walker Creek watershed, this watershed has undergone significant physical
changes in the last 150 years, including the construction of a system of large reservoirs by Marin
Municipal Water District, past agricultural land use and logging. Despite these changes,
Lagunitas Creek is thought to be one of the best coho salmon streams on the California coast,
and steelhead runs remain relatively stable as well.
Physical watershed changes have not been analyzed in as much detail as in other watersheds in
the project area covered in this report. Most studies on Lagunitas Creek have focused on the
condition of the fishery, particularly the effect of MMWD’s water impoundments on coho
salmon and steelhead. Conclusions drawn in some of these studies, commissioned by MMWD
as required by the State Water Board, have been criticized by environmental groups for focusing
too heavily on the effects of sedimentation while minimizing the importance of water flow.
Fisheries assessments and recommendations from surveys conducted during the 1980s are
included in the report.
This report found that no existing studies or anecdotal information on physical watershed
changes, stream condition or fish habitat and population for small tributaries on the east side of
Tomales Bay (Millerton Gulch, Grand Canyon, Tomasini Canyon, and unnamed tributaries) is
available. The report notes that resource values of these smaller streams seem to have been
B. Lagunitas/Olema Creek Sub-Watershed
In 2003, the Point Reyes National Seashore prepared the DRAFT Point Reyes National
Seashore Fire Management Plan. In this report, information is presented for coho salmon adult
escapement from National Park managed lands in Marin County.
Historic and current data on coho and steelhead populations for Lagunitas, Olema, and Pine
Gulch Creek watersheds have been gathered as part of the National Park Service’s (NPS) Coho
salmon and Steelhead trout Restoration Program (CSRP) and the Marin Municipal Water
District. Through the CSRP, the NPS has established a detailed fisheries monitoring program
that is carried on through support from the Natural Resource Challenge Inventory and
Monitoring Program, as well as monitoring support through California Department of Fish and
Game managed grant programs.
- 17 -
According to their summary, for most drainages, monitoring has focused on coho salmon, but
includes equivalent information for steelhead trout. Differences between steelhead trout and
coho salmon life cycles are pertinent to conservation efforts. While virtually all coho in project
area watersheds have an 18-month freshwater life cycle, steelhead juveniles may migrate to the
ocean after 18-months or extend freshwater residence for up to three years.
Estimates for adult coho escapement (numbers of spawning coho), were derived using the Peak
Live plus accumulated Dead (PLD) index method, in which the highest count of living fish found
in a single survey is added to the cumulative number of dead fish counted up to that time. The
PLD index provides a minimum count of spawning fish in a season, based upon actual field
observation. While the PLD index is best when peak numbers are counted, visibility and flow
conditions are highly variable and can affect the quality of a field survey. The PLD is interpreted
as an indication of spawning success, along with other monitoring parameters including redd
counts, summer juvenile densities, and smolt outmigration, it can be used to as an indicator of
NPS finds that review of historical spawner abundance data supports anecdotal evidence of
declining numbers of coho over the last 50 years. This corresponds to a similar trend region-
wide. Since the mid-1990s, current monitoring effort shows that populations of both coho
salmon and steelhead trout, while fluctuating, within the project area, remain persistent, and are
considered stable. A summary of spawning survey data for the Lagunitas Creek watershed is
presented in Table 1. Coho Spawning Survey Data for Overall Lagunitas Creek Watershed.
Table 1. Coho Salmon Spawning Survey Data for Overall Lagunitas Creek Watershed
Year Number of Survey Area PLD Total Total New Source
Surveys (km) Indexc Carcasses Redds
1982/83a 6 22.4 n.a. n.a. 139 Bratovich & Kelly 1988
1983/84a 6 22.4 n.a. n.a. 44 Bratovich & Kelly 1988
1991/92a 1 20.0 n.a. n.a. 41 Wise 1992
1995/96b 10 36 290 n.a. 86 Trihey & Assoc. 1996
1996/97b 8 36 525 92 254 Trihey & Assoc. 1997
1997/98b 10 36 241 112 360 MMWD, PRNS
1998/99b 10 36 147d 34 227 MMWD, PRNS
1999/00b 14 36 496d 65 220 MMWD, PRNS
2000/01b 14 36 380d 130 338 MMWD, PRNS
2001/02b 15 36 463d 146 375 MMWD, PRNS
2002/03b 13 36 463d 60 175 MMWD, PRNS
a/ Does not include Olema Creek and its tributaries.
b/ Includes Olema Creek and its tributaries.
c/ PLD Index = Peak Live and Cumulative Dead Index; n.a. = not available.
d/ Mainstem Lagunitas estimate based on total live coho observations and may include repeat sightings of same fish
MMWD = Marin Municipal Water District data; PRNS = Point Reyes National Seashore data
Devil’s Gulch has the longest period of spawner survey records for the Lagunitas Creek
watershed. CDFG biologist Eric Gerstung and warden Al Giddings noted live coho and
- 18 -
steelhead observations from 1948 to 1977. Consultants for MMWD conducted surveys from
1982-84 and 1995-97. PRNS expanded the sampling area further upstream in 1996-97. Prior to
1982/83, no more than two surveys were conducted in a single season and carcasses and redd
data were not consistently collected. Coho numbers had dropped by the 1990s, with PL index
values between 1995/96 and 2002/03 ranging from 10 to 78 fish.
Cheda Creek, a Lagunitas Creek tributary, has been surveyed since 1996/97 by PRNS to detect
the presence or absence of coho. Surveys were during peak migrations of coho in nearby
drainages, when passage and attraction flows were sufficient and water clarity was not limiting.
Coho presence in this creek appears to be sporadic, with no spawning activity detected during the
winters of 98/99 and 00/01. However, coho spawning may be increasing, with four live fish and
three redds seen in ‘01/02 and two fish and two redds in 02/03.
Until recently, much of the creek’s potential spawning area was blocked by a failed sediment
control structure. Construction of a fish passage structure consisting of a series of stepped pools
was completed in 2000. Fencing to exclude cattle from 2.5 km of the creek above and below this
structure has been completed. During fall, 2000, juvenile coho were observed in the project area.
In anticipation of future spawning activity resulting from greater access to suitable habitat,
monitoring of coho and steelhead juveniles on Cheda Creek will continue to be implemented.
The perennial section of Olema Creek has been systematically surveyed for live adult coho,
carcasses, and redds since the winter of 1994/95. Results have shown considerable variability
from year to year. As in other creeks in the Lagunitas drainage, Olema Creek had a high count
for coho salmon in the winter of 1996-97, with a PLD Index value of 174. Numbers fell
considerably below this level for the following three years, but in 2000/01 they rebounded, with
a PLD index value of 103 fish, total carcasses numbering 65, and a total redd count of 86.
Surveys have also been conducted on tributaries of Olema Creek and its headwaters, which is the
section of creek above 17.4 km from its mouth. These surveys have confirmed spawning activity
in five of the tributaries and in the Olema Creek headwaters. Except for the John West Fork and
Quarry Gulch, coho observed have been within a few hundred meters of the mainstem.
The John West Fork (aka Blueline Creek) is the most significant of the Olema Creek tributaries,
having a greater average flow and more potentially suitable spawning habitat (2.2 km) than any
other. A sharp drop below a culvert under Highway 1 previously limited access to most of the
spawning habitat; during the two winters from 1997 to 1999 only 9% (3 of 33) of the total coho
observations in the creek were above the culvert. In 1999, a structure was constructed to aid fish
passage through the culvert. In the following four winters, 75% of the total coho observations
(146 of 194) were above the culvert. As part of this project, fencing to exclude cattle from 1 km
of the creek was installed.
Starting in 1997, the CSRP has undertaken intensive survey work on Olema Creek to assess
salmonid habitat condition and reproductive success. The focus of the CSRP is to correlate
salmonid abundance at three life stages with habitat conditions to ascertain limiting factors on
overall abundance. Index sites have been established along stream reaches representative of fish
habitats and electrofishing is being used to determine juvenile coho and steelhead numbers.
- 19 -
Results will be used to prioritize habitat restoration efforts and buffer threatened salmonid
populations against potentially detrimental environmental conditions.
The Salmon Protection and Watershed Network has completed an Inventory of Select Migration
Barriers in the San Geronimo Sub-Watershed (Spring 2002) evaluating 57 human-made
structures (34 culverts, 13 dams, and 10 miscellaneous structures) and 4 natural features at 59
sites on 13 creeks. These creeks include Woodacre, North Fork San Geronimo, Bates, Deer
Camp, Creamery, Larsen, Blueline, Arroyo, Barranca, El Cerrito, Montezuma, Cintura and
Barnabe. The inventory evaluated salmonid passability in the Lagunitas Creek watershed, and
all but one creek (Barnabe Creek) are located in the headwaters of the San Geronimo watershed.
Where applicable, length, width and height above the streambed, a sketch and photo(s) were
collected at each structure. The cost of repair at each site was categorized as high or low. The
length of available habitat above the structure was measured and its quality for salmonid use was
categorized as high or low based on availability of spawning gravels, pools, woody debris and
In addition, previously collected data on current and historical use by salmonid species was used
to determine if current structures are impediments or complete barriers to upstream migration.
Previous or current monitoring of sites during low flow water conditions were used to determine
if structures were impediments or complete barriers to downstream migration of juveniles.
Recommended repairs are described for each site.
According to SPAWN’s inventory, repair of all sites would result in improved passage to
approximately 7,458 meters of spawning habitat, and repair of the top ten sites would improve
passage to 2,856 meters, 1,098 meters of which is currently completely inaccessible to
The Salmon Protection and Watershed Network (SPAWN) published Sedimentation from
Unpaved Roads in the San Geronimo Sub-Watershed in 2002. This report includes the results
of field surveys by crews that were conducted between March and June 2002. The crews
surveyed a total of 11,241 feet (2.13) miles of dirt and gravel ‘Non Maintained County Road’
and private roads, and 22 stream crossings in the San Geronimo sub-watershed. Based on these
surveys, and estimated 21,097 cubic yards of sediment have been delivered to the creek from
these roads while calculations estimate that 758 cubic yards will be delivered to the creek system
in the next 10 years.
Of the 22 stream crossings, SPAWN found that 11 are in need of repair. Failure of all 22 stream
crossings would resulted in an estimated additional 6539 cubic yards delivered to the creek
system. Since the Regional Water Quality Control Board has officially listed this watershed as
- 20 -
impaired for pathogens, nutrients and sediment, it is critical to address these roads and to prevent
further unnecessary degradation to habitat of threatened salmonid populations. SPAWN
recommends that before this process commences, surveys are completed on the roads that were
not included in their initial effort (~50%).
SPAWN also recommends that a collaborative process between government agencies now
gaining expertise in road maintenance and report to reduce sedimentation, SPAWN and/or any
other local community organizations interested in this problem, begin to work with local
landowners to begin a process to remove the source of sedimentation.
The Salmon Protection and Watershed Network (SPAWN) published Recommendations for the
Protection and Enhancement of Salmonid Populations and their Habitat in Samuel P. Taylor
Park, Marin County, California in August 2001. In this report, SPAWN summarizes coho and
steelhead population information for Lagunitas Creek, and presents recommendations that were
jointly crafted with California State Parks for the protection of these salmonids.
The Lagunitas Creek watershed has been the focal point for coho recovery in Marin County as
the current coho population is estimated to represent 10 percent of all wild California coho
surviving today. According to the report however, Lagunitas Creek coho have been reduced by
90% since the 1940’s, when estimates of the annual coho and steelhead populations in the
Lagunitas Creek watershed were 6,000. Annually, the coho population is currently estimated at
approximately 500 adults that return to the system each year to spawn, which is one of the most
robust runs left in the state. Specific impacts to the Lagunitas coho habitat include loss of habitat
(over 50% since the 1940’s) due to dam construction and migration barriers, sedimentation and
destruction of riparian habitat by development and land use practices, trampling of redds by
human and animals, pollution of streams, changes in hydrology leading to non-natural water
flow, water diversion from creeks, water withdrawal from reservoirs, and groundwater wells.
SPAWN notes that several scientists and agency personnel have expressed the view that
protection and restoration of the Lagunitas Creek watershed coho salmon population is critical to
recovery of the entire central California coho ESU.
To protect and restore the salmonid habitat in Lagunitas Creek watershed, SPAWN presents a
series of recommendations for habitat enhancement that include:
• improve horse and hiker crossings at the confluence of Devils Gulch and Lagunitas
• minimize the construction and impacts of weirs build inside of the State Park;
• improve understanding and protection of importance of woody debris; and
provide educational outreach as a means to protect and enhance stream habitat.
- 21 -
In April 2001, Marin Municipal Water District published the Juvenile Salmonid Population
Monitoring Report, Lagunitas Creek, Marin County, California Fall 2000 (MMWD 2001).
This report summarizes data collected during the fall of 2000 by Marin Municipal Water District
(MMWD) staff based on a capture and release electro-fishing survey for coho salmon and
steelhead trout in Lagunitas and San Geronimo creeks, and in Devil’s Gulch between Oct. 2 and
Oct. 31, 2000.
This survey is conducted annually and was performed in accordance with MMWD’s Aquatic
Resources Monitoring Workplan for the Lagunitas Creek Drainage, Marin County, California.
Thirteen pre-established points were sampled, and capture data were used to compute total
abundance (population size) and densities (number of fish per unit length of stream) for coho and
steelhead. In 2000, MMWD surveyed every pool and run habitat unit in Lagunitas Creek and
Devil’s Gulch by snorkeling prior to electro-fishing. The results were compared to similar
surveys conducted between 1970 and 1999 at the same sampling sites to track trends in the coho
and steelhead populations over time. In addition, habitat conditions at the thirteen sites were
documented by MMWD and generally found to be similar to the conditions documented in 1999,
with one exception. At one site a large bay tree had fallen into the pool habitat and helped to
form a large debris jam. The large number of coho observed at this site represented 30% of the
year’s catch of coho and significantly influenced the coho population estimate.
A total of 157 juvenile coho were captured from all sites during the survey, and MMWD
estimated a population of 4,684 juvenile coho in the system, and when adjusted to the normal
survey area in the population analysis prior to 1999, the juvenile coho population estimate is
4,281. According to MMWD records, this is the lowest estimate in the past eight years. For this
year class, which includes the populations surveyed in 1982, 1985, 1988, 1994, and 1997, this
year’s coho density (the average for all surveyed streams) was the lowest recorded since 1982.
The population estimate for Devil’s Gulch was the lowest in eight years and the estimate for San
Geronimo Creek was also near an eight-year low. The 1999/2000 coho spawning run was of
average size, so the low juvenile population was surprising. MMWD has no evidence of
unusually high juvenile mortality during the spring and summer, but an alternative explanation
may be the destruction of redds due to high winter stream flows. A high proportion of coho
redds were built in the main stem of Lagunitas Creek in 1999/2000. Relatively high stream
flows in Lagunitas Creek in February 2000 may have scoured many of these redds. Whatever
the cause, it appears that this year class has experienced a sharp decline.
MMWD captured 1,913 juvenile steelhead, consisting of 1,748 young-of-the-year and 165 older
steelhead (1+steelhead, 1-3 years old). They estimate a population of 59,196 juvenile steelhead
in the system. This is one of the highest MMWD estimates to date, with only the estimates of
1998 and 1999 being higher. Unlike the coho, the later-spawning steelhead had access to
tributaries and many may have spawned after the highest winter stream flows. According to
MMWD, the steelhead population appears to be robust and growing in all of the surveyed creeks.
Stream habitat types are summarized in this report as follows. There were seven sampling sites
on Lagunitas Creek and overall habitat composition in 1998 and 1999 was composed of 8%
riffle, 30% run, and 62% pool while habitat composition of the sampled sites in 2000, was
composed of 8% riffle, 34% run, and 58% pool. There were four sampling sites on San
- 22 -
Geronimo Creek and overall habitat composition when last surveyed in 1998 was composed of
12% riffle, 14% run and 74 % pool with sampled site in 2000 consisting of 13% riffle, 10% run,
and 77% pool. There are two sampling sites on Devil’s Gulch and overall habitat composition
in 1998 included 37% riffle, 7% run, and 57% pool with the composition of sampled sites in
2000 being made up of 30% riffle, 10% run, and 60% pool.
The Marin Municipal Water District completed the Lagunitas Creek Coho Salmon Spawner
Survey Report 2000-2001 in April 2001. This report presents the findings of coho salmon
spawner surveys on Lagunitas Creek between Oct. 30, 2000 and Feb. 2, 2001. Surveys were
conducted weekly on Lagunitas Creek between Tocaloma Bridge and Peters Dam. They also
conducted surveys on San Geronimo Creek starting on Dec. 7, 2000 and on Devil’s Gulch
starting on Jan. 11, 2001. These surveys were coordinated with staff from the National park
Service Coho and Steelhead Restoration Program, who conducted spawner surveys on Olema
Creek. This year MMWD conducted one survey on Lagunitas Creek between Nicasio Creek and
Tocaloma. Staff from the Salmon Protection and Watershed Network and volunteers from Trout
Unlimited also surveyed six tributaries of San Geronimo Creek.
MMWD observed the first coho in Lagunitas Creek on Oct. 30, 2000. The majority of coho
observations and redd construction in the Lagunitas Creek drainage occurred in the month of
January. During the surveys, MMWD observed a total of 204 redds and 320 live coho. They
observed 119 of these redds and 181 of the coho in Lagunitas Creek, 56 redds and 76 coho in
San Geronimo Creek, and 11 redds and 24 coho in Devil’s Gulch. The remaining 18 redds and
39 coho were observed in tributaries to San Geronimo. They also took fin and muscle samples
from 15 of the 33 carcasses found in Lagunitas Creek, San Geronimo Creek, and Devil’s Gulch.
According to the report, three of these carcasses were likely chinook salmon, but this has not yet
been confirmed. Samples will be sent to the National Marine Fisheries Service (NMFS) office in
Santa Cruz for genetic analysis. They terminated spawner surveys after Feb. 2, 2001 when the
coho spawning run appeared to have ended and steelhead observations began to outnumber coho
The report finds that the 2000/01 year’s spawning run was roughly the same size as the previous
year’s run, but not as strong as the runs of 1996/97 and 1997/98. Last year MMWD observed
203 redds and 568 coho. In 1996/97 and 1997/98 they observed 254 and 253 redds respectively.
Most of the fish that spawned this year were descendants of fish that spawned in 1997/98.
Under the minimum streamflow requirements mandated by the California State Water Resources
Control Board order WR95-17, MMWD ensured upstream migration flows of 35 cfs for three-
day periods. Releases from Kent Lake were conducted for these upstream migrations flows
starting on Nov. 28, Dec. 1, and Jan. 1. According to this report, the 2000/01 upstream migration
flows were more than sufficient to allow fish passage but did not appear to be effective at
encouraging coho to swim upstream.
- 23 -
In May 2000, Marin Municipal Water District completed the Habitat Typing Survey Report for
Lagunitas Creek, San Geronimo Creek, and Devil’s Gulch, Marin County, California 1992-
1999. As part of its efforts to improve salmonid habitat, MMWD began habitat typing of
Lagunitas Creek in 1992. In 1995 the State Water Resources Control Board mandated periodic
habitat typing as part of the SWRCB Order WR95-17. Habitat typing surveys of Lagunitas
Creek were conducted in 1992, 1997, 1998, and 1999 using MMWD and California Department
of Fish and Game protocols. Habitat typing surveys of San Geronimo Creek and Devil’s Gulch
were conducted in 1995 and 1998. While results differed between surveys, the general finding
of the surveys are:
• Pools are the most common habitat type in Lagunitas Creek, particularly downstream of
Nicasio Creek. Riffles comprise a fairly consistent 8-18% of Lagunitas Creek habitats.
• Devil’s Gulch contains the highest percentage of riffle habitat of the creeks surveyed.
• Shelter for fish is most abundant in the downstream sections of Lagunitas Creek,
particularly in the form of undercut banks, terrestrial vegetation and woody debris. Large
woody debris is uncommon upstream of the Tocaloma Bridge, as well as in San
• Gravel and cobble were the dominant substrates throughout Lagunitas Creek. Sand, silt
and clay substrates are also common in Lagunitas Creek downstream of Devil’s Gulch
and throughout San Geronimo Creek.
• The effects of flooding from the 1997-98 El Nino include an overall widening of the
creek, reduced sand, silt and clay substrates accompanied by increased gravel, and
decreased woody debris cover.
• The dominant vegetation on Lagunitas Creek (surveyed in 1997 and 1998) was deciduous
trees, mostly willow and alder species. Herbaceous cover, coniferous trees and shrubs
were dominant to lesser degrees. Habitat units with predominantly bare banks were
almost nonexistent along the surveyed creeks.
• Dominant bank vegetation differed between upstream and downstream halves of San
Geronimo Creek. Herbaceous vegetation was dominant along more than 40% of the
downstream half of the creek while only 13% in the upper half. Shrubs were far more
common along the upstream half of the creek.
According to MMWD, the data show that the Lagunitas Creek drainage has adequate salmonid
habitat but also that some habitat elements could be improved through habitat restoration. Sand,
silt and clay substrates are common in Lagunitas and San Geronimo Creeks and woody debris is
relatively scarce upstream of Tocaloma Bridge. The report states that these deficiencies are
currently being addressed by reducing sediment inputs and by adding large woody debris and
spawning gravels to the creek, and that the data presented in this report will provide a baseline
for quantifying the expected improvements in salmonid habitat resulting from these efforts.
- 24 -
C. Walker Creek Sub-Watershed
The Walker Creek Watershed Enhancement Plan (2001), was developed by the Marin
Resource Conservation District and landowners to guide the selection and implementation of
projects to restore and conserve the natural habitats in the Walker Creek watershed. This plan
includes three primary components: a list of goals and next steps developed through community
participation, recommendations for reducing sediment based on an erosion site inventory, and
recommendations for enhancing riparian habitat based on a survey of existing and historic
riparian plant communities.
The report states that the watershed is home to several endangered and threatened species,
including the tidewater goby and the freshwater shrimp. Walker Creek once supported both
steelhead and coho salmon runs. Although declining, steelhead are still present, particularly in
the area near the confluence of Chileno and mainstem Walker Creeks. DFG electroshocking of
this area in the summer of 1997 found both young-of-the-year and older steelhead. Coho
sightings have been very rare in the last fifteen years with the last two occurring in 1992 and
1998. Fisheries studies undertake in the 1970s and 1980s indicated that sedimentation and high
temperatures were limiting salmonid populations.
The MRCD’s landowner outreach effort generated five goals for the enhancement of the Walker
1. Support a strong agricultural economy
2. Provide clear, factual information on the issues facing Walker Creek.
3. Help landowners implement land management practices that support a healthy
4. Provide education for the public.
5. Work with regulatory agencies to reduce the burden on the watershed’s private
The erosion inventory identified 196 sites on 58% of the watershed below Soulajule Reservoir
and Laguna Lake where landowners granted access. Gullies and headcuts accounted for 56% of
the sites, streambanks for another 28%. The remaining sites consisted of road erosion and slides.
Each site was described and evaluated for erosion activity, the potential for future sediment loss,
access, and repair costs. The field inventory also identified possible repair strategies for each
site. Of the 196 sites, 59 received a high priority for erosion repair based primarily upon their
capacity to deliver sediment to aquatic habitat. These 59 sites were ranked into eight groups
depending on their impact to salmonid habitat.
The riparian assessment makes six broad recommendations and then identified site-specific
enhancement opportunities. These recommendations are:
1. Revegetate high and medium priority sites with cooperative landowners.
2. Manage livestock access to creeks, especially during the wet season.
3. Control invasive exotic species.
4. Protect intact sections of riparian corridor.
5. Maintain drainage structures such as culverts and ditches to prevent additional
erosion in stream areas.
- 25 -
6. Avoid depleting instream pools.
In a memo written by Bill Cox, District Fishery Biologist for Sonoma and Marin, for the
California Department of Fish and Game on October 14, 2001, no coho salmon were found in
Walker Creek. Cox used a modified “ten pool protocol” sampling ten pools in each of two
reaches with a Smith-Toot type XII electro-fisher, making a single pass through each pool. The
three reaches planned for the survey were in an area where he expected to find coho if they were
in the stream (one reach was not accessible). These reaches approximated the locations where a
total of 5 coho were collected in October 1981 by John Emig. The total number of steelhead for
the two reaches sampled (20 pools) was 172, and stickleback, roach and sculpin were also
Cox noted that despite the very dry winter of 2000-01, which had resulted in very low to no flow
in many streams, Walker Creek had a high summer flow (about 2.5 cfs) because of releases from
Soulajule Reservoir. Runs, and even some pools, had a distinctly fast flow. Runs and pools
were not well distinguished. Water temperatures ranged from 55 to 60 degrees, while
temperatures in August and September are more likely in the high 60s and 70s.
D. Historical Salmonid Planting in the Tomales Bay Watershed
According to California Department of Fish and Game (CDFG) records from 1960-1990 for
coho planting in the Lagunitas Creek watershed, CDFG and Point Reyes National Seashore
planted a total of approximately 400,000 coho in Lagunitas (Papermill) Creek, Halleck Creek,
and Nicasio Creek (or their tributaries) from various hatcheries. The details for each release are
presented in Appendix B: Lagunitas Creek Watershed Coho Planting History. The large
majority of these fish were from Noyo River hatchery stock, and have therefore influenced the
local genetics of the Lagunitas Creek coho as a result. Information on steelhead planting in the
Lagunitas Creek watershed is not available at this time.
Walker Creek watershed was also planted with coho and steelhead on different occasions
during this period, and will be planted again during January 2004 with approximately 100 adult
coho by the California Department of Fish and Game. The following table (Table 2. Summary of
Walker Creek Salmonid Planting 1970-1980), created by the Marin Municipal Water District,
summarizes plantings according to California Department of Fish and Game salmonid stocking
records for Walker Creek.
- 26 -
Table 2. Summary of Walker Creek Salmonid Planting 1970-1980
YEAR MONTH SPECIES # STOCKED AGE CLASS
1977 March Coho Salmon 15,411 Yearlings - 15/lb
1979 April Coho Salmon 15,300 Yearlings - 15/lb
1980 May Coho Salmon 18,363 Yearlings - 11.3/lb
1982 May Steelhead 30,000 Fingerlings - 500/lb
1983 May Steelhead 36,600 Fingerlings - 600/lb
1984 March Steelhead 13,000 Yearlings - 6.5/lb
1984 ? Steelhead 40,000 ?
1988 July Coho Salmon 22,000 Fingerlings - 100/lb
a. Source: Sid Poe, pers. comm., California Department of Fish and Game (March 26, 1998).
b. The Coho Salmon were likely from DFG’s Noyo River stock (this needs to be confirmed).
c. The second planting of Steelhead in 1984 were from hatch boxes in Lagunitas Creek.
Within the Tomales Bay watershed, and in the State of California, the Lagunitas/Olema
Creek watershed is one of the most important creek basins for wild coho in the Central
California Evolutionarily Significant Unit (ESU), and provides valuable habitat to steelhead
trout and other important aquatic species as well. Although these creeks have been degraded
by human activities over the last century, the Salmon Protection and Watershed Network,
Trout Unlimited, Tomales Bay Association, Marin Municipal Water District, Point Reyes
National Seashore, California Department of Fish and Game, Marin County, San Francisco
Bay Regional Water Quality Control Board, and others have worked to protect, assess and
enhance salmonid habitats in this watershed for the last few decades. Much of the Lagunitas
and Olema Creek watershed is in public landownership, or is maintained as open space by the
Marin Municipal Water District, Point Reyes National Seashore and Golden Gate National
Recreation Area and therefore provides increased opportunity for resource protection,
enhancement and monitoring to improve salmonid habitats.
The large majority of the Walker Creek watershed is in private landownership, and agriculture
is the primary landuse. Within this watershed, the salmonid fishery has been significantly
degraded over the last century and little quantifiable information exists for coho and steelhead
populations. It is thought that coho no longer return to the Walker Creek watershed; however
steelhead, in unknown numbers, are thought to return annually and other important aquatic
species are found in this system. Habitat assessments have been periodically conducted during
the last 20 years by the California Department of Fish and Game, Marin Municipal Water
- 27 -
District, Regional Water Quality Control Board, and the Marin Resource Conservation District.
Additionally, habitat restoration projects are on-going and are primarily facilitated by the Marin
Resource Conservation Service and Natural Resource Conservation Service on private
agricultural lands in this sub-watershed.
In summary, during the last decade, habitat and sediment assessments have been conducted in
Lagunitas, Olema and Walker creeks and on some of their primary tributaries. A small minority
of the other small tributary creeks that flow directly to Tomales Bay along the east and west
shores have ever been surveyed, and none of them are regularly monitored to evaluate salmonid
populations or potential habitat. In general, these creeks are considered to be either too steep or
too short to provide valuable coho habitat; however strong steelhead runs have been described by
long-term residents that once fished in Millerton, First and Second Valleys, and some of the
other creeks. A limiting factors assessment for salmonids will be completed in the
Lagunitas/Olema sub-watershed during the next 3 years. In addition, the Point Reyes National
Seashore will be synthesizing and analyzing salmonid information during 2004 as part of their
on-going restoration and monitoring program.
The following preliminary recommendations are based on the information that is currently
available about the condition of salmonid populations and their habitats in the Tomales Bay
watershed, and local expertise about what is needed to move forward toward enhancing coho and
1. Maintain exiting fisheries, habitat and streamflow monitoring efforts by the National
Park Service, Marin Municipal Water District, Salmon Protection and Watershed Network,
Tomales Bay Association, and others. Include winter, spring and summer monitoring activities,
and efforts to evaluate trends in different life stages of coho and steelhead in the Tomales Bay
2. The reports that have been annotated here provide valuable although sometimes conflicting
information. An important next step is to critically review, synthesize and analyze the data
that is available for coho and steelhead populations and habitats in the Tomales Bay watershed.
More specifically, based on this analysis, the preliminary Lagunitas/Olema sub-watershed
recommendations for restoration, assessment and monitoring actions need to be reevaluated
based on the upcoming Limiting Factors Analysis. Also, Walker Creek watershed information
needs to be integrated and analyzed to identify assessment, restoration and monitoring priorities
and needs. Similarly, additional fish population monitoring and habitat surveys (using the
Department of Fish and Game’s Salmonid Habitat Inventory Methods, Level III or comparable
protocol) are warranted to increase our understanding of the current populations and needs of
salmon and steelhead in this watershed.
- 28 -
3. As a result of current data on habitat conditions and salmonid populations, preliminary
conclusions indicate the following restoration priorities need to be undertaken in the near
• barriers to fish passage;
• sediment source reduction;
• unpaved road improvements to reduce sediment based on field surveys and priority sites
(San Geronimo sub-watershed and in the rest of Marin County);
• large woody debris enhancement; riparian management;
• winter high flow refugia;
• floodplain restoration; and
• water diversions.
The Lagunitas/Olema Creek watershed is the highest priority within the Tomales Bay
watershed for future fisheries restoration attention and funding due to its existing coho and
4. As a result of data gaps in assessments and surveys that have been conducted, preliminary
conclusions indicate the following priorities need to be addressed in the near future:
• continue habitat surveying (using the Department of Fish and Game’s Salmonid Habitat
Inventory Methods, Level III or comparable protocol) and water quality monitoring in
subwatersheds with coho populations (Lagunitas, San Geronimo mainstem, Devil's
Gulch, Olema, etc.);
• initiate habitat surveying (using the Department of Fish and Game’s Salmonid Habitat
Inventory Methods, Level III or comparable protocol) including water quality monitoring
in other streams that have not been surveyed previously or only minimally (San
Geronimo Creek tributaries, Walker Creek, eastern and western Tomales Bay tributaries,
• out migrant fish surveys in the lower Lagunitas/Olema sub-watershed and in lower
• assess over-wintering salmonid habitat in the Lagunitas/Olema sub-watershed;
• assess spawning gravel quantity and quality in the Lagunitas/Olema sub-watershed;
• conduct fish population surveys in the Lagunitas/Olema and Walker sub-watersheds to
establish basin-wide estimates;
• continue streamflow analysis to evaluate thresholds for sediment transport, scouring of
redds, and responses to timed water released in the Lagunitas/Olema sub-watershed;
• evaluate downstream temperature related responses to releases from Soulajule Reservoir
in the Walker Creek sub-watershed;
• assess estuarine habitat and temperature;
• continue mercury monitoring and evaluate effects to salmonids in the Walker Creek
• conduct floodplain studies to evaluate historical and current function and use by
salmonids in the lower Lagunitas/Olema and Walker Creek sub-watersheds.
5. Facilitate completion of a comprehensive Limiting Factors Analysis of Lagunitas/Olema
sub-watershed, including estuarine and marine aspects of this system based on Phase I of the
- 29 -
Lagunitas Limiting Factors Assessment. Based on this assessment, reevaluate and identify
restoration priorities for this system.
6. Maintain outreach activities to promote increased awareness of salmonid restoration efforts,
future needs and opportunities for involvement in the Lagunitas/Olema and Walker creek sub-
watersheds. Specifically, cultivate relationships with private landowners to promote increased
participation in restoration and monitoring efforts, and to increase access to streams in the
watershed. Support efforts with Walker Creek landowners to increase local willingness to
participate in salmonid recovery efforts.
These recommendations indicate the types of project proposals that local organizations, agencies
and the Watershed Council will continue to seek funding for in 2004 and beyond. The ongoing
programs through the Point Reyes National Seashore, Salmon Protection and Watershed
Network, Marin Municipal Water District, the California Department of Fish and Game, and the
Marin Resource Conservation District to survey salmonid populations, assess habitat and
monitor changes will be critical to our long-term understanding of trends and needs in the
Tomales Bay watershed fishery. Additionally, the continuation of research and assessment to
develop good science must be conducted simultaneously with on-the-ground restoration, and
monitoring will be critical to evaluate the effectiveness of our efforts and areas in need of future
A matrix for project selection and prioritization has been developed by the Council and its
partners to strategize future restoration efforts in the Tomales Bay watershed (see Appendix A:
Salmonid Restoration Project Ranking Criteria for Use in the Tomales Bay Watershed). This
matrix shall be used to rank potential projects in Lagunitas, Olema, and Walker creeks and in
other tributaries in the Tomales Bay watershed. The highest scoring projects shall receive
prioritization for potential funding that is available. Increased attention is warranted in the
Lagunitas/Olema watershed due to the significance of the remaining coho population there, and
the critical restoration needs that have been identified to date.
- 30 -
LIST OF PARTNERS AND PROJECT SELECTION CRITERIA FOR FUTURE
I. Organizations and Agencies Participating in Salmonid Restoration and
Assessment Activities in the Tomales Bay Watershed
There are many local organizations and agencies that are working to assess, restore and protect
salmonid habitats in the Tomales Bay watershed. These efforts are being increasingly
coordinated to maximize the effectiveness and potential long-term success of often costly and
time consuming actions to address in-stream and upslope issues that are degrading salmonid
habitats and water quality. To support this coordination, the strategy and matrix to rank potential
project is presented in Appendix A: Salmonid Restoration Project Ranking Criteria for Use in the
Tomales Bay Watershed. These criteria and the scoring process are intended to identify projects
that will have the highest likelihood of benefiting current salmonid populations, those with the
best potential for long-term success, and opportunities for partners to work together to evaluate
priorities and plans at the sub-watershed scale. Through the Tomales Bay Watershed Council,
partners have participated in crafting this scoring matrix, and will meet periodically to use it.
The primary parties working to assess, restore and protect salmonid populations in the Tomales
Bay watershed include:
• The California Department of Fish and Game’s (CDFG) Fisheries Restoration Grant
Program has contributed $700,000 towards planning, assessment, and restoration projects
within the Tomales Bay watershed during the last five years. This funding has produced
the Walker Creek Watershed Plan and subsequent riparian fencing, revegetation,
alternative water source and erosion control implementation projects in partnership with
the Marin RCD; sediment source reduction in the Lagunitas Creek watershed in
partnership with the Marin County Open Space and Marin Municipal Water Districts;
riparian fencing in Lagunitas Creek watershed in partnership with the Tomales Bay
Association and National Park Service; riparian enhancement in Lagunitas Creek
watershed in partnership with Marin Municipal Water District; and salmon and steelhead
trout monitoring in Lagunitas Creek watershed in partnership with the National Park
Service. Most recently, CDFG has funded the Tomales Bay Watershed Council to
continue its outreach, education, and watershed planning and assessment efforts.
• The California State Coastal Conservancy (Conservancy) has been actively
participating in conservation and restoration efforts in Tomales Bay for over 25 years.
Working with partners such as MALT, the Marin RCD, NPS and Marin County, the
Conservancy continues to fund projects to restore and enhance the agricultural and
natural resource values of West Marin. The Conservancy has been an active participant
in watershed planning in Tomales Bay since the early eighties. Other Conservancy
projects have included acquisitions of agricultural and conservation easements
throughout the watershed, erosion control, livestock fencing and stream revegetation
projects, an assessment of fish passage barriers in Marin County, and an assessment of
on-site septic systems and their impact on coastal waters.
- 31 -
• California State Parks manages significant reaches of Lagunitas Creek in addition to
lands adjacent to Tomales Bay. Past efforts include: development of a General Plan that
addresses Tomales Bay water quality, resource management, and land acquisition; water
quality monitoring; on-going erosion control projects; and maintenance of all facilities at
Samuel P. Taylor, Tomales and Millerton State Parks.
• During the last three decades, the County of Marin (County) has provided protection for
riparian areas and fisheries through the Countywide Plan, and creek and grading
ordinances. These policies were the subject of review in 1997 when FishNet 4C was
formed to focus on improving county practices and policies affecting fisheries, and
resulted in the formation of a Marin County fishery protection team. The County has also
created a training program for county road maintenance, and a program to address fish
barriers. The County has recently completed an inventory of fish passage barriers
throughout all of Marin County, in addition to work on specific projects to enhance
• The Marin Municipal Water District (MMWD) is a significant landowner and manager
of natural resources in the Lagunitas Creek watershed. MMWD diverts water from the
Lagunitas Creek basin to provide water supply for over 185,000 residents in southern and
central Marin County. These diversions are regulated by the State Water Resources
Control Board (SWRCB). In its WR Order 95-17, the SWRCB ordered MMWD to
develop and implement a 10-year sediment and riparian management plan with the
following goals: provide an appreciable, long-term improvement to streambed conditions
in Lagunitas Creek for the benefit of coho salmon and steelhead; and enhance instream
fish habitat in Lagunitas Creek between Kent Lake and Tocaloma through riparian
vegetation management and by placement of woody debris. Ongoing monitoring
activities by MMWD include: annual juvenile and spawner salmonid surveys; streambed
monitoring surveys; habitat typing surveys along the mainstem of Lagunitas Creek,
Devil's Gulch, and San Geronimo Creek. MMWD has also convened the Lagunitas
Creek Technical Advisory Committee, made up of agency, environmental groups, and
other interested stakeholders. This group meets quarterly to advise the MMWD Board on
policies related to Lagunitas Creek, to review study designs and results, and to advise on
proposed enhancement projects.
• Since 1959, the Marin Resource Conservation District (MRCD) has endeavored to
conserve and enhance the watershed’s natural resources, including soil, water, vegetation
and wildlife while maintaining a viable agricultural economy. Over 100 conservation
projects have been completed to this end, including gully repairs, streambank
stabilization, road repairs and manure management projects. Over 3.5 million dollars
have been spent on such projects - in addition to critical watershed planning, studies and
assessment work- to improve water quality, aquatic and terrestrial wildlife habitats.
Currently, ranchers in the Walker Creek watershed are nearing completion of 6
contiguous miles of stream restoration. In the next three years, the MRCD will be
administering 2 million dollars to continue conservation efforts in the Tomales Bay
watershed, including a limiting factors assessment for salmonids and freshwater shrimp
in the Lagunitas Creek watershed.
- 32 -
• The Point Reyes National Seashore (PRNS) has a long-term interest in the health of
Tomales Bay and its watershed. PRNS annually surveys juvenile salmonids and
spawning adults, assesses habitat conditions, and continues instream and upslope
restoration project to enhance salmonid habitats and to mitigate migration barriers in
Olema Creek and tributaries, parts of Lagunitas Creek and tributaries, and in Pine Gulch
Creek through their Coho Salmon and Steelhead Trout Restoration Project. In addition,
to guide its actions and promote coordination with other agencies, PRNS developed the
Tomales Bay: Guidelines for Protection and Use (2001). PRNS has secured funding for
riparian protection fencing along Olema Creek, initiated a planning process for the
restoration of wetlands at the southern end of the bay, and established a water quality
• The Salmon Protection and Watershed Network (SPAWN) has a long-term
community-based program to assess, restore and protect coho and steelhead populations
in the San Geronimo Valley. Their efforts include migration barrier and sediment
assessments, water quality monitoring, spawner and juvenile surveys, juvenile relocation
efforts during summer, and instream habitat restoration projects. Existing water quality
assessment undertaken by SPAWN in partnership with RWQCB focuses on examining
levels of nutrients, pathogens and septic residue (MBAS) in the Lagunitas watershed.
SPAWN has also undertaken a systematic characterization of salmonid habitats in the
San Geronimo System to ascertain the specific needs for placement of woody debris
• The San Francisco Bay Regional Water Quality Control Board (RWQCB) has been
the driving force behind remediation and monitoring of mercury from the Gambonini
mine in the bay and tributaries. RWQCB staff have recently completed a draft pathogen
Total Maximum Daily Load (TMDL) report identifying pathogen sources to Tomales
Bay, and will be working on a TMDLs for mercury for Walker Creek. The RWQCB has
administered considerable funding for projects ranging from nonpoint source pollution
reduction (e.g. erosion control to septic improvements) to limiting factors assessments in
the Lagunitas Creek watershed for salmonids and freshwater shrimp. In the more distant
past, the RWQCB instituted regulations on discharges into Tomales Bay, put all
treatment plants in the watershed under permits, and required improvements on dairy
facilities. During the next 3 years RWQCB will administer over $1.3 million in the
Tomales Bay watershed for aquatic habitat assessment and improvements in the
Lagunitas Creek watershed, and nonpoint source reduction projects in the Tomales Bay
watershed on dairies and ranches.
• The Sierra Club (Club) is Marin County’s oldest and largest environmental organization.
The Club, through its partnership with other concerned organizations in the Save
Tomales Bay Committee, petitioned the State Water Board to protect Lagunitas Creek,
which resulted in the 1995 Order for the Marin Municipal Water District to maintain
minimum water flows, reduce sedimentation, increase woody debris, and monitor fish
populations. The Club continues to monitor MMWD’s compliance with the 1995 Order
through its participation on the Lagunitas Technical Advisory Committee. Recently, the
- 33 -
Club, again through its partnership in the Save Tomales Bay Committee, negotiated an
agreement with the North Marin Water District that further protects salmonid populations
in Lagunitas Creek. The Club is active in numerous creek, wetland and salmonid issues
throughout Marin County.
• The Tomales Bay Association (TBA) has conducted a salmonid monitoring and
restoration program since 1986 on Olema Creek. TBA installed livestock exclusion
fencing and planted thousands of willows to improve riparian habitat. TBA has also
sponsored projects and assisted the NPS with other fencing projects on Cheda and
Devil’s Gulch streams, and has published numerous educational documents. TBA was a
major participant in the State Water Resources Control Board (SWRCB) Hearings which
culminated in the 1995 SWRCB Order 95-17 to protect coho salmon, steelhead and other
aquatic species in Lagunitas Creek; and TBA recently negotiated, with invaluable
assistance from Trout Unlimited, a settlement agreement with North Marin Water District
establishing a precedent-setting, first-time dedication of appropriative water rights for
instream habitat purposes.
• Trout Unlimited’s (TU) mission is to conserve, protect and restore North America’s
trout and salmon fisheries and their watersheds. TU accomplishes this mission on local,
state and national levels with an extensive and dedicated volunteer network. TU has
provided such support in the Tomales Bay watershed during the last 20-years, with
special attention and focus given to coho populations in the Lagunitas/Olema Creek
- 34 -
Hecht, B. 1983. Substrate enhancement/sediment management study, Lagunitas Creek, Marin
County-Phase IIIb: Sediment transport and bed conditions, 1979-1982: H. Esmaili &
Associates consulting report prepared for the Marin Municipal Water District, 173 p.
Kashiwagi, J.H. 1985. Soil Survey of Marin County. U.S. Department of Agriculture, Soil
National Park Service. 2001b. Coho and Steelhead Restoration Project Annual Section 10
Permit Data Report: July 1, 1999 – June 30, 2000. Coho and Steelhead Restoration
Niemi, T.M, N.T. Hall, 1996. Historical changes in the tidal marsh of Tomales Bay and Olema
Creek, Marin County, California. Journal of Coastal Research. 12(1): 90-102.
PRNS (Point Reyes National Seashore, NPS). 2001. Tomales Bay Guidelines For Protection
and Use. Point Reyes National Seashore. Point Reyes Station, CA. 33 p.
Prunuske Chatham, Inc. 2001. Walker Creek Watershed Enhancement Plan. Marin Resource
Conservation District, Point Reyes Station, CA. 55+.
Smith, S. V. and J.T. Hollibaugh. 1997. “Annual Cycle and Interannual Variability of Ecosystem
Metabolism in a Temperate Climate Embayment.” Ecological Monographs 67(4): 509-
State of California Department of Health Services. 2002. Twelve-Year Sanitary Survey Report:
Shellfish Growing Area Classification for Tomales Bay, California. Technical report no.
02-04. 58 p.
TBWC (Tomales Bay Watershed Council). 2003. Tomales Bay Watershed Stewardship Plan: A
Framework for Action. Point Reyes Station, CA. 137 p.
UCCE (University of California Cooperative Extension). 1995. Final report of the Marin Coastal
Watershed Enhancement Project.
Wehrhaftig, C. and J.R. Wagner. 1972. The geologic setting of Tomales Bay. In Tomales Bay
Study: A Compendium of Reports. Prepared for the Conservation Foundation.
- 35 -
California Department of Fish and Game. 2003. Recovery Strategy for California Coho Salmon
(Oncorhynchus kisutch): A Report to the California Fish and Game Commission.
Species Recovery Plan Report 2003-1. 786 pp.
Ettlinger, E., Andrew, G.M. and Aviva Rossi. 2001. Juvenile Salmonid Population Monitoring
Report, Lagunitas Creek. Marin County, California, Fall 2000. Prepared for Marin
Municipal Water District, Corte Madera, California.
Ettlinger, Eric and G. M. Andrew. 2001. Lagunitas Creek Coho Salmon Spawner Survey Report
2000-2001. Prepared for the Marin Municipal Water District, Corte Madera, California.
Ettlinger, E., G.A. Andrew, G. Aull. 2000. Habitat Typing Survey Report for Lagunitas Creek,
San Geronimo Creek, and Devil’s Gulch, Marin County, California 1992-1999. Prepared
for the Marin Municipal Water District, Corte Madera, California.
Institute for Fisheries Resources. 2003. Final Draft KRIS West Marin-Sonoma Database.
Compact Disk, contact (707) 822-9428.
National Park Service. 2003. Internal draft Point Reyes National Seashore Fire Management
Plan. Point Reyes National Seashore 400+ pages.
NMFS (Weitkamp, L. A., T. C. Wainwright, G. J. Bryant, G. B. Milner, D. J. Teel, R. G. Kope,
and R. S. Waples). 1995. Status review of coho salmon from Washington, Oregon, and
California. U.S. Dept. of Commerce, NOAA Tech. Memo. NMFS-NWFSC-24, 258 p.
(Download in PDF format 6.9 MB)
NOAA Southwest Fisheries Science Center, Garza, J.C. and E. Gilbert-Horvath. 2003. Report on
the Genetics of Coho Salmon (Oncorhynchus kistuch) held at Warm Springs (Don
Clausen) Hatchery for Recover Efforts in the Russian River. Santa Cruz Laboratory,
NOAA Southwest Fisheries Science Center. 2001. Status Review Update for Coho Salmon
(Oncorhynchus kisutch) from the Central California Coast and the California portion of
the Southern Oregon/Northern California Coasts Evolutionarily Significant Units. Santa
Cruz Laboratory, California.
Prunuske Chatham, Inc. 2001. Walker Creek Watershed Enhancement Plan. Prepared for the
Marin County Resource Conservation District, Point Reyes Station, California.
Ross Taylor and Associates. 2003. Marin County Stream Crossing Inventory and Fish Passage
Evaluation, Final Report. Prepared for the County of Marin, Dept. of Public Works.
Tomales Bay Watershed Council. 2003. Tomales Bay Watershed Stewardship Plan: A
Framework for Action. Point Reyes Station, California. 137 pp.
- 36 -
University of California Cooperative Extension. 1995. The Marin Coastal Watershed
Enhancement Project. Novato, California.
Walder, Reuven. 2002. Sedimentation from Unpaved Roads in the San Geronimo Sub-
Watershed. Prepared for the Salmon Protection and Watershed Network, Forest Knolls,
Walder, Reuven. 2002. Sedimentation from Unpaved Roads in the San Geronimo Sub-
Watershed. Prepared for the Salmon Protection and Watershed Network, Forest Knolls,
Walder, Reuven. 2001. Recommendations for The Protection and Enhancement of Salmonid
Populations and Their Habitat in Samuel P. Taylor Park, Marin County, California.
Prepared for Ron Angiers, Samuel P. Taylor Park Supervisor, Ken Leigh, State Park
Superintendent, Marin District and Samuel P. Taylor Park Ranger, Interpretive and
Walder, R., Corsini, M. and Steiner, T. 2002. Inventory of Select Migration Barriers in the San
Geronimo Sub-Watershed. Prepared for the Salmon Protection and Watershed Network,
Forest Knolls, California.
- 37 -
DRAFT Salmonid Restoration Project Ranking Criteria
for Use in the Tomales Bay Watershed
1. The Decision Making Tree is intended to guide project selection by evaluating 4 primary
considerations associated with each project: current salmonid populations (placing
greatest importance on streams with coho in them each year rather than those without
fish, or with fish only sporadically); landowner commitment to long-term success;
whether there are currently remnant salmonid populations that can benefit from
restoration efforts; or if the project will enhance potential future salmonid habitat.
2. The Numeric Project Ranking Criteria include the basic issues that should be considered
when evaluating and prioritizing salmonid restoration projects. Not all of the criteria
need to be considered at the local level as some of the grantors (e.g. DFG, RWQCB, etc.)
have their own criteria and protocols, landowner agreements, etc. that must be used and
these agencies should be included in evaluating the projects along with the local members
of a field team.
I. Decision Making Tree for HIGH, MEDIUM and LOW priority categories
Tier 1: High priority criteria- must answer yes to both questions #1 and #2
1. Does the sub-watershed currently support a wild coho/steelhead population or does the
project remove a migration barrier preventing the sub-watershed from supporting these
species (yes), stay in Tier 1 and proceed to question #2;
• (no): go to Tier 2
2. Will there be a signed landowner agreement indicating a commitment to future project
success and achieving restoration goals (yes), stay in Tier 1.
• (no) but the landowner will allow a partnering organization/community group to
fulfill this responsibility: go to Tier 2
• (no) the landowner does not agree to monitor and maintain the
condition/effectiveness of the project nor will allow anyone else to do so: go to Tier
Tier 2: Medium priority criteria- must answer yes to question #1
1. Does the sub-watershed support wild coho/steelhead but in remnant numbers that do not
constitute an important population, or is this Project one component of a clearly defined
long-term watershed plan (that includes specific restoration objectives) to restore a
salmonid population (yes), stay in Tier 2 and proceed with the numeric ranking criteria;
• (no): go to Tier 3
Tier 3: Low priority criteria- must answer yes to question #1
1. Did this sub-watershed historically support a population of wild salmonids that is no
longer present, and will the Project increase potential habitat for future reestablishment
by salmonids (yes), stay in Tier 3 and proceed with the numeric ranking criteria;
• (no) do not recommend the Project for funding at this time.
- 38 -
II. Numeric Ranking Criteria
Prescreening sub-watershed specific criteria to guide restoration efforts based on locally
collected information and local restoration goals and objectives:
1. Fisheries: sub-watershed supports population(s) of wild anadromous salmonid
species based on multi-year surveys and best available sampling methodologies (3
Watersheds or sub-watershed currently supporting populations of wild coho and/or
steelhead should be protected to the best degree possible.
3 pts. – Populations of coho and steelhead are currently present.
1 pts. – Population of 1 of the above fish species is currently present.
0 pt. – Neither of the above fish species is currently present.
2. Fisheries: potential to address limiting factors identified in the sub-watershed (10
Project will address factors negatively affecting salmonid population dynamics including:
water quantity, water quality, riparian dysfunction, excessive sediment, spawning, over-
winter habitat, summer rearing, escape cover, estuary, passage, other.
One point given for each limiting factor addressed by the project up to 10 possible
3. Fisheries: project addresses a risk posed to coho population (5 possible pts.)
The project will address risk(s) posed to the coho population that is currently supported
by the sub-watershed.
5 pts. - Project addresses a critical risk that has been identified, and the potential benefits
of the project and mitigation of the threat/impact to the coho population is clearly
3pts. – Project addresses a potential risk to the coho population and the potential project
benefits are likely to improve habitat.
1 pt. – Project may benefit coho population by mitigating a risk that has been described in
4. Fisheries protection: project protects best remaining salmonid habitat and/or
occupied habitat (5 possible pts.)
The project will protect the best remaining/currently occupied salmonid habitat in the
5 pts. – The project will help protect the best remaining/currently occupied salmonid
habitat in a sub-watershed that is currently supporting coho.
3 pts. – The project will help protect the best remaining/currently occupied salmonid
habitat in a sub-watershed that is currently supporting steelhead.
1 pt. – The project will protect potentially high quality salmonid habitat in a creek/sub-
watershed that may provide habitat to salmonids in the future.
- 39 -
5. Human impacts: is current and future planned landuse adjacent to the project
consistent with restoration goals? (3 possible pts.)
Consider the adjacent and upslope landuses that potentially affect the project location,
and evaluate if adequate measures are in place to mitigate degradation to project area.
3 pts. – The project is located in an area where adjacent lands are protected in perpetuity
(e.g. via an easement, public lands, etc.), and planned landuse is consistent with salmonid
2 pts. – The project includes a landowner agreement with at least a 10-year management
plan to avoid adjacent landuse activities that could negatively impact the potential future
success of the project, or appropriate mitigation strategies are employed (e.g. filtration
buffers, recharge areas, etc.) to avoid potential degradation of salmonid habitat
1 pt. – The project includes a landowner agreement with at least a 3-year management
plan to avoid adjacent landuse activities that could negatively impact the potential future
success of the project and/or potentially degrade the quality of the salmonid habitat.
0 pts. – The project does not include a landowner agreement with a management plan.
6. Priority: the project is based on an assessment/study prioritizing restoration needs
(5 possible pts.).
Is the project identified in a prior study that has evaluated the restoration needs of the
sub-watershed? As a Tomales Bay watershed assessment comparing restoration
opportunities between the Lagunitas and Walker Creek watersheds (and other small
tributaries) has not been conducted, smaller scale assessments are needed to guide
restoration at the sub-watershed scale.
5 pts. - The project is identified as a high/critical priority project in a pertinent (still
accurate) watershed assessment/study to evaluate the aquatic community and the
condition of both upstream and downstream salmonid habitat.
3 pts. – The project is a medium priority that has been identified in a pertinent (still
accurate) watershed assessment/study but warrants attention.
1 pt. – The project is a low priority that has been identified in a pertinent (still accurate)
watershed assessment/study but warrants attention.
7. Watershed: is the project located in an area that is contiguous with diverse, high
quality habitat? (5 possible pts.)
Projects that are adjacent to high quality salmonid habitats, or projects that increase
connectivity between such habitats, are priorities in restoring healthy sub-watersheds.
Reconnecting habitats needed by different life stages should be considered at the sub-
watershed scale, and disconnected habitats (e.g. barriers to migration thereby reducing
access to potentially high quality habitat) represent opportunities for recovery and should
receive priority ranking for restoration.
5pts. – The project clearly defines restoration objectives, and how methods and project
outcome will restore connectivity to diverse, high quality salmonid habitat.
3 pts. – The project defines restoration objectives, linking of methods and project
outcome(s) to restoration of connectivity and diverse, high quality salmonid habitat are
not entirely clear.
1 pt. – The project defines restoration objectives, potential benefits of the project are
- 40 -
8. Watershed: Is the project to occur in a biologically significant sub-watershed as
defined by TBWC (5 possible pts.)
Is the project to occur in an ecologically healthy sub-watershed that currently supports
biologically significant populations of salmonids with diverse, native assemblages of
aquatic organisms, or is this a historically significant sub-watershed with restoration
5 pts. – The project is in a biologically significant sub-watershed and restoration
objectives clearly connect potential project benefits with needs of the system.
3 pts. – The project is in a biologically significant sub-watershed and restoration
objectives will likely enhance potential habitat.
1 pt. – The project is in a historically significant sub-watershed, and restoration
objectives will enhance potential salmonid habitat and reestablishment of other aquatic
9. Watershed: Does the project help restore an impaired watershed process which
results in a critical impairment in stream geomorphic or biological function (5 pts.).
Is the project going to restore a watershed process (e.g. restore infiltration capacity of
watershed and lead to recharging of the groundwater), which will enhance the biological
diversity and dynamics that are necessary to sustain a healthy aquatic community?
5 pts. - The project will have a substantial beneficial effect on the watershed processes.
3 pts. – The project will have a moderate effect on watershed processes.
1 pt. – The project will have a minor effect on watershed processes.
10. Water Quality: project will mitigate water quality and/or sediment associated issues
adjacent to high quality habitats (5 possible pts.)
Do project objectives address water quality and/or sediment associated issues effecting
5 pts. – The project objectives address significant water quality and/or sediment related
issues (in the water column, streambed, or in other ways limiting salmonid populations)
in a sub-watershed that currently supports coho.
3pts. – The project objectives address water quality/sediment related issues in a sub-
watershed that currently supports steelhead.
1 pt. – The project objectives will likely improve water quality in a sub-watershed that
may support salmonids currently, or will expand potential habitat in the Tomales Bay
- 41 -
More detailed criteria to be evaluated with agency/technical support:
11. Design addresses causes not symptoms (5 possible pts.)
Does the project design address the sources or causes of habitat degradation?
5 pts. – Project design objectives and expected outcomes or products are clearly stated
and follow acceptable protocol, and relationship to cause of aquatic habitat degradation
3 pts. – Project design objectives and expected outcomes appear adequate however the
source or cause of aquatic habitat degradation is not clearly addressed in the proposal,
some inadequacies in approach.
1 pt. – Project design is not clearly stated and/or cause of habitat degradation poorly
12. Design is sound, effective and appropriate for site (5 possible pts.)
Are the proposed actions, methodologies and procedures the most technically appropriate
and environmentally sensitive choices for addressing the stated problem?
5 pts. – Objectives and expected outcomes are clearly stated and related to the technical
approach; methodologies and proposed actions are technically sound and their
applicability is well demonstrated; timeframe is reasonable.
3 pts. – Objectives and expected outcomes appear related to technical approach; proposed
actions have some inadequacies or their applicability is not well demonstrated; project
objectives may not be accomplished within the planned timeframe.
1 pt. – Objectives are not clearly stated; methodologies are not technically sounds and
their applicability has not been demonstrated; project cannot be completed within
13. Monitoring- the project includes a monitoring and maintenance plan (5 possible
pts.) that has been developed in cooperating with the landowners. We recognize that
many private landowners do not know about the best monitoring and maintenance
approaches for salmonid restoration projects, and will require technical support to
develop an appropriate plan. Future monitoring and maintenance however, is critical to
the likelihood of success and should be part of the landowner agreement. DFG has
monitoring protocols, etc.
5 pts. – The proposed project should clearly describe an appropriate and feasible
monitoring and maintenance plan to evaluate project effectiveness while ensuring
necessary maintenance in the future.
3 pts. – The proposed project describes basic on-site monitoring to ensure appropriate
construction while meeting future maintenance needs.
1 pt. – The proposed project describes minimal monitoring and maintenance, but
recognizes the need for site visits to evaluation project condition and effectiveness after
- 42 -
14. Permitting- is permitting complete? (3 possible pts.)
Have the necessary environmental permits been secured thereby allowing project
construction to proceed immediately as funds are available?
3 pts. – All required permits are complete.
0 pts. – Permits are still required.
15. Funding- matching funds/in-kind contribution (3 possible pts.)
The landowner and/or applicant is providing a significant funding contribution to the total
3 pts. – Matching funds/in-kind contribution is at least 50% of total project cost
2 pts. – Matching funds/in-kind contribution is at least 25% of total project cost
1 pt. – Matching funds/in-kind contribution is between 10-20% of total project cost
Total possible points = 72
Approximate breakdown: 14% project design, 32% condition of salmonid fishery,
4% matching funds, 4% potential adjacent human impacts, 7% monitoring plan,
4% timely permitting, 7% predetermined priority, 21% habitat condition in sub-
watershed, 7% project to improve water quality
- 43 -
- 44 -
Lagunitas Creek Watershed Coho Salmon Planting History
- 45 -
- 46 -
Comprehensive List of Salmonid and Related Aquatic References
for the Tomales Bay Watershed
- 47 -