Adaptation Strategies for Trout, Salmon and Their Watersheds During by dsn16018

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									            Adaptation Strategies for Trout, Salmon and Their Watersheds
                               During Climate Change

                   Jack E. Williams, Amy L. Haak, and Nathaniel G. Gillespie
                              Trout Unlimited, Arlington, Virginia


Introduction

The rapid pace of climate change has brought about unprecedented environmental change with
significant ramifications for the nation’s freshwater systems and the biodiversity they support.
Shifts in the timing of hydrologic events already have begun as rainfall patterns vary and warmer
temperatures come earlier in the year. In snowmelt dominant systems this means earlier peak
flows and lower than normal summer flows exacerbating competition for over-allocated water
resources when demand is greatest.

Warmer winter temperatures also contribute to depleted groundwater supplies. More
precipitation comes as rain rather than snow, augmenting late winter stream flows with runoff
instead of gradually soaking into the ground throughout the spring and summer as the mountain
snowpack melts. Loss of this source of late season cold water further compounds the effects of
reduced summer stream flows and rising temperatures, potentially creating a lethal situation for
coldwater species as well as creating opportunities for diseases and parasites previously limited
by coldwater to spread. High-altitude lakes also are experiencing the ill-effects of warming
temperatures as nuisance algae is proliferating, reducing dissolved oxygen to potentially lethal
levels for fish.

Although disturbance events such as wildfire, flood, and drought always have been an integral
part of shaping landscapes and fish communities, climate change is escalating the frequency and
magnitude of these events in a manner that is increasingly detrimental to aquatic systems. At
higher elevations and more northerly latitudes, fire is a growing concern as snowmelt begins
earlier in the spring and snow accumulation occurs later in the fall, increasing the length of the
fire season while warmer temperatures dry out the forests. Fire can have an immediate impact
on aquatic systems with some fires resulting in loss of riparian habitat and acute spikes in water
temperature that may rise to lethal levels. Long-term consequences include increased erosion
and sedimentation as floods generated from rapid rainfall run-off in a burned watershed. Winter
flooding also is expected to increase, particularly in the mid-elevations where warmer mid-
winter temperatures result in more rain-on-snow events. Summers, especially in the Southwest,
are expected to suffer from extreme and prolonged drought due to increased heat related
moisture loss. As hydrologic patterns change from snowmelt to rainfall and as the intensity of
storms increase, rivers will transport more sediment, erode their banks, and scour the beds more
readily. Taken together, climate change will alter habitat conditions substantially.

Coldwater fishes are particularly vulnerable to these environmental changes. Their dependence
on an abundant supply of cold, clear water through-out all stages of their complex life histories
makes them highly susceptible to changes in water temperature. Physiological impacts from
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warm water include slower growth rates and increased stress due to reduced levels of dissolved
oxygen and greater susceptibility to toxins, parasites and disease. Ultimately, prolonged
exposure to unsuitable water temperatures can result in death.

Warmer water also may lead to changes in the timing of migration while reduced summer and
fall flows make it more difficult for adult fish returning from the ocean to negotiate waterfalls
and other barriers as they move upstream to spawn. Spawning behavior of trout and salmon is
dependent on the high concentrations of dissolved oxygen found in cool water. Fall spawners
such as bull trout are particularly susceptible to late season low flows and warmer water
temperatures. Many other trout species have evolved to time their spawning behavior around
snowpack melt when there is an abundance of cold water. However, uncharacteristic winter
flooding and erosion events could be severe enough to scour incubating eggs from spawning
beds. Even the food supply of trout and salmon is at risk as warmer water triggers the earlier
emergence of mayflies and other aquatic insects in western streams. This change in peak flow
timing has resulted in smaller and fewer insects so less food is available for fish.

Trout and salmon are very resilient species and have adapted to major climatic and
environmental fluctuations over their history. Today however, much of their habitat has been
severely degraded by land conversion and resource extraction while dams and other instream
barriers block the movement of remaining migratory populations. As a result, most native trout
and salmon now occupy less than 30% of their historic habitat and have lost accessible migratory
corridors that allowed them to disperse to suitable areas when existing habitat was degraded. For
many trout species, range contraction has been most pronounced at the lower elevations in the
valley bottoms and along the margins of their historic ranges. The loss of low elevation and low
latitude populations is particularly significant since these populations likely had genetic
adaptations to warmer conditions. The loss of that genetic diversity may limit a species’ future
ability to adapt.

In addition to the adverse effects of land use practices, some fisheries management strategies
also have contributed to fragmentation and isolation. In order to protect genetically pure
populations from competition, predation, and hybridization with introduced species, native trout
populations purposefully have been isolated in small headwater streams above artificial barriers,
essentially eliminating migratory life history forms. While these barriers protect the populations
from introduced species, they also prevent escape from disturbance events such as fire and flood
and preclude post-disturbance recolonization after the watershed recovers. Many of the
remaining genetically pure populations are so small that they are at risk of collapse due to
genetic isolation as well as environmental disturbances.

Unless action is taken to restore resistance and resilience to climate change within our
watersheds, significant declines of coldwater fisheries are expected, including major losses of
genetic, life history, and ecological diversity, all of which are key to these species adapting to
future environmental changes. In this chapter we first describe the basic responses of trout and
salmon to climate change and then explore constraints and opportunities for improving the future
prospects of coldwater fishes and the watersheds they depend on. We will describe a framework
for protecting, reconnecting, and restoring watersheds for salmon and trout that can be utilized
for almost any freshwater fisheries. Then, we will apply this framework to three case studies,

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including a salmon-producing river system along the West Coast, a native trout watershed in the
Rocky Mountains, and a native brook trout drainage in the East. Although each watershed and
fishery is unique in many respects, we believe that they often share common problems and
opportunities. Restoration of any watershed depends upon a solid scientific understanding of the
existing condition and underlying sources of stress, a good appreciation of the broader river
basin context, a desire to involve broad constituencies of land owners, managers, and interests in
problem solving -- and a dedicated group of citizens striving for a common goal of restored
natural systems. Adapting watersheds and fish populations to climate change is a long-term
undertaking that not only will yield benefits to fisheries but also to local communities that rely
on watersheds for a dependable supply of clean water and protection from the most damaging
floods and drought.

Coldwater Fish Responses to Climate Change

The role of habitat condition

Existing habitat condition plays a crucial role in determining the severity of climate change
impacts. Scientists have demonstrated that streams located in high quality watersheds can
improve in response to high spring flows. On the other hand, impacts from disturbances such as
floods and drought can be more intense and frequent in streams draining from degraded
watersheds. In some classic experiments, Luna Leopold, a former Chief Hydrologist with the
U.S. Geological Survey, compared runoff events in watersheds in natural condition versus those
modified by urbanization and agriculture. He found that runoff from more modified watersheds
was “flashier” and tended to peak earlier and at higher levels. Channelized streams, dense road
networks, and larger amounts of constructed landscapes all tend to make watersheds more flood-
prone. In these degraded watersheds, the additional stress of climate change may further reduce
channel stability, accelerate erosion, increase peak flows, and decrease base flows.

In coldwater fisheries, water temperature that is within the preferred range of salmonids,
generally 50o F to 65o F, often is considered the most critical characteristic of high quality
habitat. Sources of cold, clean water, such as groundwater, springs, coldwater seeps, spring-fed
creeks, and streams flowing from heavily forested north-facing slopes are disproportionately
important to coldwater-dependent species because they often provide ideal spawning and
juvenile rearing conditions as well as refuge from extreme drought, high summer temperature,
and winter extremes. Many of these springs and spring-fed creeks also are prized by humans for
their consistent sources of water, and unfortunately have been degraded by agricultural,
residential, and industrial uses. As the earth warms, these coldwater refuge areas will play an
increasingly important role in providing resilience to coldwater aquatic ecosystems and native
trout and salmon, and will demand our attention as the focus of restoration and protection efforts.

Additional characteristics of high quality habitat include connectivity among a variety of habitat
types, including areas with silt-free gravel for successful spawning, and riverine habitats with
deep pools and adequate woody debris to provide cover from predators and refuge from floods,
droughts and winter conditions. In general, more complex and diverse habitat conditions will
favor long-term sustainability of native fish communities.


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Habitat loss and degradation has limited the historic distribution of most native salmonids, with
some western trout species and subspecies having lost 80-90% of their historic habitat. Eastern
Brook Trout Joint Venture regional experts identified “poor land management associated with
agriculture, urbanization and stream fragmentation” among the top reasons that a brook trout life
cycle component, typically successful spawning is eliminated. Warm water temperature, which
typically results from loss of riparian vegetation, alteration of the natural hydrology, and
degradation of stable channel conditions, also was identified as a top problem for brook trout in
the East. Pat Flebbe’s studies on Appalachian wild trout populations found that brook trout, as
well as introduced brown and rainbow trout, habitat in the southern Appalachians currently are
limited primarily by water temperature, which in turn has been altered from historical conditions
by forest fragmentation, agriculture, road networks and urban and residential development.
Bruce Rieman and colleagues from the U.S. Forest Service note that threatened bull trout already
are severely limited in their historical distribution by habitat loss and fragmentation. Bull trout
are especially dependent on high quality cold water habitat.

Climate change threatens to further limit and fragment existing native salmonid populations,
particularly in systems and regions where trout and salmon exist on the margins of suitable
habitat. The increase in summer air temperatures will likely reduce the amount of suitable
habitat and force fish upstream to smaller streams at higher elevations where the risk of floods,
drought and wildfire may lead to local extirpations. Increased demand for scarce water
resources, loss of riparian habitat, and floodplain development will further degrade aquatic
systems and reduce their resistance to climate change.

The role of non-native species

In addition to habitat condition, the presence of non-native species has significant implications
for the ability of native trout and salmon populations to survive climate change. The presence of
invasive species often compounds problems associated with degraded habitat as many exotics
thrive in altered warm-water environments.

Already introduced warm-water species likely will expand their ranges as water temperatures
warm and aquatic habitat degradation increases. Introduced coldwater species are likely to
continue to impact native salmonid populations as well. In the intermountain West, introduced
non-native trout populations will continue to compete with native cutthroat trout for shrinking
coldwater habitat, while rainbow trout in particular are likely to continue introgression with
native cutthroat subspecies as suitable habitat shrinks and warmer water temperature encourages
expansion of rainbows and hybrid trout into colder headwater areas currently supporting
genetically pure cutthroat.

Changes to a natural hydrologic and sediment regime by reservoir impoundment and tailwater
releases generally benefit introduced fish species that tend to be better adapted to lotic, warm
water environments and therefore often displace native salmonid populations that evolved to
thrive in a riverine setting. Another invasive species benefitting from tailwater habitats is the
nuisance algae commonly referred to as didymo. Non-native species, both flora and fauna, will
continue to take advantage of impoundments and compromised river systems, using altered
habitats as a base from which they can spread and alter native ecosystems. A similar situation

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occurs in reservoirs stocked with numerous predatory species that can disperse both upstream
and downstream into more riverine areas occupied by native salmonids. The biological
modification of our native ecosystems will amplify the impacts of climate change to further
stress indigenous trout and salmon populations.

The question of why some fishes are more likely to survive climate change than others depends
on numerous factors, including the general nature of their habitat requirements, ability to
withstand varied environmental conditions, and ability to disperse into new areas. Species such
as smallmouth bass have proven remarkably adept at flourishing in coldwater lakes, ponds and
larger river systems in the East (eastern brook trout habitat) and in the West (cutthroat trout and
redband trout habitat). In some western rivers, introduced predators are reported to consume up
to 40% of migrating juvenile salmon, indicating that the impact of severe non-indigenous
species, including smallmouth bass, walleye and northern pike.

Limitations of Existing State and Federal Programs

The management of streams and rivers pose numerous management constraints and opportunities
compared to terrestrial systems. The British ecologist H.B.N. Hynes is well known for his
imperative that ‘you can’t divorce a stream from its valley’. Watersheds, rather than the stream
itself, provide a more ecologically sound management focus. One of the common reasons that
stream restoration efforts fail is that they did not consider the broad watershed context in which
restoration projects were conducted. Failures of this nature are likely to become more common
as existing stressors in the watershed become magnified by climate change.

Because of the long, linear nature of streams and rivers, they tend to cross numerous agency
jurisdictions and land ownerships, a circumstance that confounds efforts to manage these
systems and their fisheries in a holistic manner. As rainwater or snowmelt flows downhill and
through soils, it coalesces into streams that flow downhill into larger streams, which themselves
become tributaries to larger rivers. In this way, water can be viewed as connecting the landscape
from ridgetop to valley bottom throughout an entire basin. This connectivity is an important
ecological attribute of stream systems, yet many of our government policies focus on narrow
jurisdictions that tend to fragment and disrupt these connections.

Multiple land owners often are affected by fisheries restoration. Public lands such as National
Forests, Parks, and BLM public lands are more common in headwater and mid-elevation areas,
whereas private lands often dominate downstream rivers and valley bottoms. In the western
United States, and to a lesser extent in the East, smaller headwater streams often flow from
public lands onto private lands. In order to provide sufficient connectivity of stream systems,
multiple land ownerships and agency jurisdictions should be integrated.

Typically, federal agencies have regulations and policies that provide substantial riparian buffer
areas for stream management on public lands. Private lands, however, are governed by state and
local regulation, which often are less protective. In such situations, incentive programs available
through the Farm Bill, the Natural Resources Conservation Service or other agencies within the
U.S. Department of Agriculture, or state programs may encourage larger riparian zones. A key
to successful restoration at the watershed scale will be the ability of restoration practitioners to

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move beyond public lands restoration and conservation to develop productive and cooperative
relationships with private land owners.

On the plus side, climate change may increase our ability to form new alliances with agencies
and land owners because of shared interests in the sustainability of water supplies and the need
for natural systems to ameliorate the impacts of increasing disturbances such as drought and
floods. This may help supplement existing fisheries restoration funds, which likely will be
inadequate considering the scale of needed adaption work. For example, municipalities and
water management agencies are concerned about the potential for reduced snowpack and other
changes in precipitation patterns associated with climate change to disrupt stream flows and
water supplies. Efforts that create wetlands, restore riparian habitats, or rehydrate high elevation
meadow ecosystems will increase the water holding capacity of the watershed, which in turn,
will facilitate slower runoff and more dependable base stream flows. Floods that threaten
downstream land owners can be ameliorated by insuring that rivers have access to their natural
floodplains and that riparian zones are well vegetated. It is vital to think holistically and
examine upstream and downstream resources to fully appreciate the potential for partnerships in
stream and watershed restoration.

Watershed Framework for Adaptation Strategies

Building resistance and resilience in trout and salmon populations so they can adapt to their
changing environment requires a holistic ecosystem-wide approach. Conservation actions
should have a sound ecological basis that incorporates and promotes natural processes at the
watershed scale. Trout Unlimited’s protect-reconnect- restore-sustain framework is a
comprehensive watershed-scale strategy for securing the diversity of habitat needed by coldwater
fishes to support their complex life histories (Figure 1). Conceptually, protection strategies
typically are applied to the headwaters where the best habitat often is found on high elevation
public land, restoration occurs in the more modified valley bottoms, and reconnection joins the
upper streams to the mainstem rivers. The sustain piece of the framework speaks to the human
component and the need to engage communities and the next generation in conservation
activities in their home watersheds that not only will benefit trout and salmon, but the people
who live and recreate there as well.

For many native fishes, the headwater tributaries contain the last remaining strongholds for
genetically pure populations. These cold, clear waters are extremely important for spawning and
are integral to maintaining a consistent supply of coldwater to downstream habitats. Every effort
should be made to maintain or improve the water quality and watershed conditions of these areas
so that they will continue to provide critical refuge during times of rapid environmental change
from global warming. A critical component of protecting these habitats is protection of the
populations they support. Despite the high quality habitat generally associated with these small
mountain streams, they are particularly vulnerable to a major flood event or severe wildfire that
could wipe out the resident population. Although natural processes eventually will restore the
habitat, particularly if the system was healthy before the disturbance, the population cannot
recolonize the headwater stream if the upstream area was isolated above a barrier. Therefore,
protection of important strongholds and genetically pure populations often goes beyond simply
maintaining the status quo and may require increasing available habitat and re-establishing

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stream connectivity so fish can disperse if their habitat becomes temporarily unsuitable and then
repopulate the habitat when conditions improve. Restoring connectivity maximizes the natural
resilience of these systems and populations by allowing them to adapt to changing
circumstances.




Figure 1.  Fluvial or river migratory form (A) and resident stream form (B) of Bonneville cutthroat trout.  Restoring 
connectivity among small isolated native trout populations can restore fluvial life history forms, which will provide 
significant survival advantages during climate change because of their ability to move more freely among stream 
systems and recolonize previously disturbed habitat.  The fluvial fish also are more resistant to invading non‐native 
species because of their larger size and higher fecundity.  Photos courtesy Warren Colyer and Trout Unlimited. 



In addition to reestablishing connectivity among headwater streams, it also is important that
these high elevation tributaries are reconnected to larger downstream rivers. Connection to the
more productive valley bottom streams is critical to the reestablishment of migratory populations
and should be a cornerstone of any range-wide recovery strategy. Removing obsolete dams and
diversions and retrofitting others for fish passage will give trout and salmon access to the
diversity of habitats that healthy large rivers provide. Projects to identify and fix road culverts
that form instream barriers should be a priority because they often prevent fish from accessing
high quality tributaries. In situations where rivers run dry due to over allocation of water, efforts
should focus on incentives for leaving water in streams and maintaining a more natural flow.

Finally, reconnection actions can reach their full potential only if the habitats being reconnected
are of a quality that will support wild populations of trout and salmon. Although the valley
bottoms have sustained the most damage from human development they also hold the greatest
opportunity for restoration of channel diversity and deep pools. A comprehensive restoration
plan should include projects that address not only the in-stream habitat conditions but also the
contributing landscape. Many of the nation’s larger rivers have been disconnected from their
floodplain and riparian zones. Reestablishing the riparian corridor for bank stabilization and
shading is an important part of building resistance to climate change. Similarly, reconnecting
rivers with their floodplains is vital to restoring the natural processes that benefit water quality,
insects, in-stream conditions and fish. It also will have the added benefit of moderating effects
of flood events and wet and drought cycles. When working on valley bottom restoration it is

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important to understand what is happening upstream in the watersheds to identify sources of
sediment, rapid runoff, or diversions that have downstream implications. Local stresses such as
eroding streambanks, elevated water temperatures, or the loss of deep pools need to be dealt with
at their source, which can be on the immediate landscape and/or on parts of the landscape
significantly upstream.

There is one especially important caveat to consider when reconnecting fish populations. Non-
native invasive species pose a major threat to many native trout and salmon and provide
managers with a conundrum when attempting to reconnect headwater and mainstem habitats.
Barriers that prevent fish movement within streams may also protect upstream populations from
downstream non-native fishes. The ideal recovery plan should incorporate a portfolio of
strategies, including reconnected streams within watersheds as well as populations isolated above
protective barriers. Ironically, climate change is likely to lead to even greater concerns with non-
native fish species, including smallmouth bass, channel catfish, and other predatory species not
usually associated with trout habitat. Regardless of how connected or isolated habitats are,
monitoring and control of non-native fishes will be a crucial management requirement.

The protect-reconnect-restore-sustain strategy applied at the watershed scale will help build the
resistance and resilience coldwater fish and their habitat need for a changing future (Figure 2).
However, there still are many unknown factors related to climate change and ecosystem
response. Monitoring and evaluation are necessary components of any effective strategy to
understand complex interactions within systems. Our ability to accurately interpret relationships
between our actions and observed results will help unravel the nuances of a rapidly changing
environment.




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Figure 2.  Graphic representation of how the Protect‐Reconnect‐Restore‐Sustain strategy can be applied to upper, 
middle, and lower elevations of a watershed.  Illustration courtesy of Bryan Christie Design and Trout Unlimited. 



Common Types of Projects

Riparian Restoration. Riparian areas are among the most dynamic and biologically rich habitats
in watersheds because they form the linkage between aquatic and terrestrial systems. They
perform many critical functions for stream systems, including serving as sources of large wood,
shading and thereby cooling flows, and buffering streams from erosion, sedimentation, and
pollution that result from upslope activities. Establishing adequate riparian zones (width and
length) and restoring native vegetation are primary goals. Existing activities within these zones
that contribute pollutants, including sediment, should be removed or curtailed. Fencing is a
common method to identify riparian zones and exclude undesirable practices such as livestock
grazing. Transportation and energy corridors often need to cross streams but should not run
parallel in close proximity to streams whenever possible.

Floodplain Restoration. Floodplains are another very dynamic part of the landscape, but are
more often associated with mainstem rivers and valley bottoms. In many areas, rivers have been
disconnected from their floodplains by channelization, and the construction of levees and dikes.
During floods, channelized rivers have nowhere to dissipate high flow energy, which often
results in high rates of erosion in downstream areas. Floodplains and associated wetlands also
are a principal area of groundwater recharge, which also serves to reduce flood impacts and

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support higher base stream flows. Rivers can be reconnected to floodplains by removing or
setting back levees, removing revetment or other structural impediments to rivers overflowing
their banks. Lateral movement of rivers over time and the formation of sand and gravel bars, are
important hydrologic functions for many fish and plant communities, which can be facilitated by
providing adequate floodplain area.

Stream Reconnection. During extreme flow events or other disturbances, coldwater fish need to
be able to move freely among headwater streams, and between headwaters and larger rivers to
find adequate refuge areas. Unfortunately, many streams have been disconnected from one
another by a variety of common management actions, including road crossings, small dam
construction, and flow diversions or other flow reductions. Often, culverts were not properly
designed to provide fish passage across the range of likely flows. Most watersheds contain so
many barriers to fish movement that it will be necessary to prioritize the importance of barriers
to fish movement by at least four factors:

   1.   How complete the blockage is under various flows or time of year
   2.   Where the barrier occurs within the watershed
   3.   How much habitat would become accessible if the barrier was removed
   4.   Relative cost of fixing each problem

Poorly designed culverts can be replaced by properly designed culverts, bridges, or bottomless
archway culverts. Sometimes, baffles can be installed into existing culverts to slow water and
allow fish to pass, but often, a significant drop is present at the downstream end that signals the
need for more significant alterations. Restoring stream flows in dewatered stream segments or
downstream of diversion structures may involve finding alternative sources of water, restoring
instream flows through purchase or other agreement, increasing efficiency of water use so that
more can be left instream, or some combination of these measures. As discussed elsewhere in
this chapter, tradeoffs between removing barriers to facilitate movement of desirable species, and
the need to provide barriers to separate desired from undesirable fishes needs close attention (see
also the 2006 U.S. Forest Service General Technical Report RMRS-GTR-174 for a good
discussion of this problem). Removal of larger dams is discussed below in the Rogue River case
study.

Stream Channel Complexity. Stream channels can be restored or modified to create areas of
coldwater refuge, including deep pools; undercut banks; areas near downed logs, root wads, or
large boulders; side channel or alcove habitats; and spring inflow areas. Providing adequate
space for a river to meander can help over time to develop the kind of complex in-channel
habitat needed for cold water refuges. Large wood, whole trees with root wads, and large
boulders can be placed in streams or onto riparian areas next to streams to encourage
development of channel complexity and deep pools. Mainstem rivers or river segments that
currently contain complex channel conditions with cold-water refuges should be protected.
Alcove habitats and side channels can be constructed in areas suitable to that kind of habitat
feature.

Invasive Species Control. To manage fisheries at larger watershed scales, it will be necessary to
adequately monitor and control non-native species. Some non-native fish species or low

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population sizes of these species may be tolerable with desired management goals while other
species may need to be eliminated all together. It is important to consider that climate change
may alter long-term habitat conditions over time to favor more invasive, “weedy” species.
Population dynamics within multiple-species communities and changeable environments are
likely to be complex, which should encourage non-native species control efforts at early stages
of invasion. Chemical treatments involving piscicides (most commonly Rotenone or Antimycin)
are used to treat streams or lakes when a complete kill of fishes is desired. Various methods of
physical removal, such as electroshocking, trapping, and netting, also can be used but tend to be
less effective than chemical treatment if complete removal of a species is desired. If the desire is
to depress, rather than eliminate, a species of non-native gamefish, it may be possible to reduce
their numbers through changes in fishing regulations. Most state fish and wildlife agencies have
trained staff familiar with fish control methodology, permitting, and precautions. Regardless of
which method is chosen for removal, it is vital to ensure that the undesired fish does not again
reinvade the system, either by their own movement within a river system or by their purposeful
reestablishment by anglers or others.

Case Studies for Adapting to Climate Change

                               Eastern Brook Trout Streams:
                          Thorn Creek Subwatershed, West Virginia

Generalized Management Situation. The Eastern Brook Trout Joint Venture determined that
native brook trout currently occupy less than 50% of their historical habitat in the eastern United
States, with the primary perturbations to brook trout populations and aquatic habitat identified as
warm water temperature, livestock grazing, poor agricultural practices and degraded riparian
condition, particularly in the valley bottoms where much of the native forest vegetation has been
removed for agricultural development. The current habitat condition in Thorn Creek is
representative of existing conditions for brook trout throughout much of the East. Existing
restoration efforts in the Thorn Creek subwatershed are designed to improve livestock
management and agricultural practices on private lands and to extend native brook trout
populations and reconnect fragmented populations.

Geographic and Biological Setting. Thorn Creek and its primary tributaries, Blackthorn and
Whitethorn creeks, comprise a mountainous watershed dominated by private lands in rural
Pendleton County, West Virginia (Figure 3). Thorn Creek is a tributary to the headwaters of the
South Branch of the Potomac River, a major tributary of the Chesapeake Bay. The 32,808-acre
subwatershed is 75% forested and 25% in some form of agricultural or livestock production.
Ridgetops and steep slopes are forested and actively managed for timber and wildlife habitat and
valleys are primarily used as pasture for beef cattle, industrial chicken production, or cropped for
hay, corn and other vegetables. The geology is underlain with karst limestone and many
tributaries are spring-fed. Sixteen springs with a minimum base flow of at least 100
gallons/minute have been identified in the subwatershed.

This portion of the Upper Potomac River Highlands was heavily altered from its native forested
ecosystem beginning in mid-1750s with the arrival of the first colonial settlers and clearing of
the landscape for agriculture, timber and wood-related products. The landscape was used for

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pasture and subsistence agriculture for over a century. Conventional farming methods are
commonplace and include removal of all native vegetation across large portions of the valley
floor, including the floodplain and riparian zone of many miles of historical brook trout waters.
Other challenges include uninhibited livestock access to stream spring heads and management of
manure and other animal wastes from cattle and large-scale chicken production facilities.

Brook trout populations in the Thorn Creek subwatershed are small and isolated in the upper
tributaries, having lost the majority of migratory populations that historically occupied the larger
mainstem habitats. Along many valley bottom streams the entire riparian plant community has
been cleared and many sections have been channelized or disconnected from the floodplain by
berms constructed for agricultural development or in response to flood events. Conditions in the
valley bottoms are degraded and no longer support trout although introduced smallmouth bass
and other centrarchids with a tolerance for high water temperatures are found there. Populations
of native brook trout remain where forested hillsides and mountainous terrain limit agricultural
development, however habitat fragmentation from small dams and road culverts as well as the
legacy of past clear-cut timber harvests reduce available habitat. Limited land protection in the
subwatershed has left it vulnerable to continued agricultural production, livestock grazing, and
unsustainable timber harvest. Despite these degraded conditions, Thorn Creek has many
restoration opportunities. The forested hillsides and abundance of cold, clear spring water have
the potential to provide critical coldwater refugia for remaining brook trout.

Goals and Objectives. The overall goal of the project is to restore Thorn Creek and its tributaries
so that the subwatershed can function as a coldwater refuge and brook trout population source
within the larger headwaters of the South Branch Potomac River. Within that context, objectives
within the subwatershed are to restore degraded springs, stream channels and riparian habitats
along the entire stream network, and remove existing stream passage and water temperature
barriers so that brook trout can occupy the full extent of their historic habitat in the Thorn Creek
system.

Project Tasks. Because of the large amount of private land in the subwatershed, developing
good working relationships with landowners is integral to project success. Trout Unlimited (TU)
staff brought a watershed-scale approach to Thorn Creek and have developed conservation
agreements funded through the Natural Resources Conservation Service (NRCS) and Farm
Services Agency (FSA) incentive-based programs with 14 landowners. Requirements for
achieving riparian reforestation and water source protection include livestock exclusion fencing,
spring/well-development, water trough facilities with solar charges and solar pumps, and
instream channel structures. The majority of these best management practices are funded
through three NRCS Farm Bill programs: the Conservation Reserve Enhancement Program
(CREP), Environmental Quality Incentive Program (EQIP), and Wildlife Habitat Incentive
Program (WHIP).

Collectively to date, landowners, TU staff, and agency partners have installed over 25,000 linear
feet of fence and replanted 32 acres of riparian forest within the Thorn Creek watershed.
Projects to protect eight miles of stream via livestock exclusion and riparian reforestation are
currently under contract and waiting USDA funding. In 2007, TU staff hired three employees
for a fencing team that is dedicated exclusively to building livestock exclusion fencing. TU has

                                                 12
applied for grants for upgrade/replacement of 9 stream crossings that are partial or total fish
passage blockages to 25 stream miles of historic habitat. Resource agencies are buying into this
watershed approach focused on brook trout restoration, and subsequently have agreed to spend
$400,000 on work in Thorn Creek in the next three years.

Trout Unlimited staff works with landowners and is responsible for each project from start to
finish, including assisting with the development of conservation plans that meet agricultural
needs and benefits the aquatic environment, building fencing and related structures, organizing
riparian vegetation restoration, overseeing streambank or stream channel restoration work,
performing maintenance to the property, and monitoring. The interest from landowners and the
success of this partnership prompted NRCS to designate the watershed as a model “natural
stream channel demonstration site” for the state of West Virginia. The Eastern Brook Trout Joint
Venture has designated Whitethorn Creek as one of 10 “Waters to Watch” for 2009. Both
accolades speak to the success of this comprehensive approach that focuses on quality control
and satisfaction of the landowner.

Implementation Schedule and Costs for Target Watershed.

Step #1, Year 1. Fish and habitat inventory to more precisely define opportunities, limiting
factors, and to establish baseline conditions. Cost estimated at $30,000 for the subwatershed.

Step #2, Year 2. Hiring dedicated watershed coordinator. Project planning, developing
landowner relationships, interagency coordination, and permitting. Cost estimated at $70,000
per year ($630,000 for 9 years).

Step #3, Year 2-4. Develop conservation agreements and grant applications for private land
restoration. Cost estimated at $100,000.

Step #4, Years 3-7. Conduct on-the-ground restoration work including livestock exclusion
fencing ($200,000), development of off-stream watering ($200,000), restoration of riparian plant
communities ($200,000), and removal of high priority culverts and other barriers to fish
movement ($350,000), and maintenance work ($50,000). Total costs for restoration work are
estimated at approximately $1,000,000. Of course, each watershed has its own unique
combination of problems, opportunities, and constraints, so costs from one area to the next may
vary widely.

Step #5, throughout project monitoring and evaluation. Projects should be monitored to
determine their effectiveness and the need for maintenance work or changes in restoration
approaches. Fish populations also need monitoring to determine effectiveness of habitat
restoration and to determine the presence of invasive fish species. Monitoring costs over a 10-
year restoration program will vary, but could amount to approximately $25,000/year for a total of
$250,000.

Total costs are estimated for the Thorn Creek subwatershed over a 10-year implementation
period at $2,010,000.



                                               13
Implementation Barriers. The most significant implementation barrier to restoring the Thorn
Creek watershed is developing and maintaining trust with the private landowner community.
Historically, landowners in this region have been resistant to engaging with state or federal
agency personnel on cost-share programs. The restoration of brook trout has proven to be the
key to gaining participation from a multitude of private landowners and the creation of a
watershed-scale effort Successful restoration will continue to depend on the ability of project
proponents to facilitate enrollment of landowners in state and federal programs to improve water
quality, protect and restore riparian and instream habitat, and to reconnect fragmented aquatic
habitat. Funding represents another barrier to successful implementation of the project over the
next decade, both in terms of installing the best management practices on farmland, and in
maintaining project personnel and leadership that has proved so integral in initial restoration
efforts in the watershed.

Conservation Outcomes. When existing restoration work is completed, brook trout habitat in
the Thorn Creek watershed will have increased by 15 stream miles and resulted in recovery of
over 45 miles of connected, spring-fed stream habitat and vastly improved water quality entering
the South Fork of the Potomac River and ultimately the Chesapeake Bay. Restored riparian
communities and reconnected hydrology will reduce stream temperatures and provide increased
resilience to climate change impacts such as floods and drought.




                                               14
Figure 3.  Thorn Creek subwatershed, West Virginia, in the South Branch Potomac River Subbasin.  Nearly all lands 
within the subwatershed boundary are in private ownership.  All stream systems shown are within the historic 
range of brook trout. 
                                                           



                                                       15
                           Rocky Mountain Trout Streams:
          Cottonwood Creek Watershed, Upper Green River Drainage, Wyoming

Generalized Management Situation. In much of the West, native trout habitat has been reduced
and fragmented compared to historic distribution. As a result, remaining populations typically
occupy small headwater streams, often on public lands, and have been eliminated from larger
stream systems that are now inhabited mostly by non-native fishes. Non-natives often include
introduced trouts that would hybridize with native species if they had access to headwater areas.
Remaining habitat is fragmented by a number of small irrigation diversion dams and/or poorly-
designed culverts that prevent upstream fish movement. Instream barriers prevent movement of
native trout, but they also may prevent mixing with non-desired species. As headwater streams
coalesce into larger streams, they typically flow downstream onto public lands managed by the
BLM and/or onto privately-owned ranch land. Habitat quality often degrades with decreasing
elevation and larger order stream systems. Although the larger stream systems often provided
the best trout habitat historically, they are now more often than not, impacted by agriculture,
livestock grazing, and reduced riparian vegetation.

Geographic and Biological Setting. Our case study is from a small watershed draining the east
slope of the Wyoming Range in the Upper Green River drainage of Wyoming (Figure 4). The
entire Cottonwood Creek watershed was historic habitat for Colorado River cutthroat trout,
which are now restricted to 3 small headwater streams on National Forest lands. Numerous
instream barriers subdivide habitats and isolate trout populations into small streams that may
support only a few hundred to, at most, a few thousand fish. Most of the larger stream system is
located on private lands but BLM and state-owned lands are scattered among larger cattle
ranches. Another sensitive native fish species, the flannelmouth sucker, occurs in the watershed
but downstream from remaining native cutthroat trout. The downstream fish assemblage is a
combination of native species, such as flannelmouth and mountain suckers, and non-native
species, such as rainbow trout and white sucker. Stream channels on private lands are degraded
and simplified compared to historic conditions. Deep pools, undercut banks, and shaded stream
sides that would help ameliorate climate change impacts and provide cooler water are mostly
lacking. On the other hand, there are many restoration opportunities, but most of these will
require close coordination with and cooperation from private landowners, as well as state and
federal agencies.

Although each watershed is unique, the above setting is more or less typical of that found
throughout much of the Rocky Mountain West, including habitat for Bonneville cutthroat trout,
Colorado River cutthroat trout, Greenback cutthroat trout, Rio Grande cutthroat trout, Gila trout,
Montana Arctic grayling, and portions of redband trout, Yellowstone cutthroat trout, westslope
cutthroat trout, and bull trout habitat. In general, native trout habitat tends to be more
interconnected in the north and more fragmented in the arid southwestern states. Problems with
non-native fishes and habitat degradation are common themes through the West. Impacts from
energy development, including surface land disturbance and water quality degradation, are a
growing concern throughout many of the Rocky Mountain states. Regardless of the sources,
impacts from existing stressors will combine with climate change to produce substantially
greater cumulative impacts on watersheds and native fish populations.



                                                16
Goals and Objectives. The overall goal is to restore and protect a watershed-scale areas where
native fish conservation is emphasized by protecting remaining high quality habitats,
reconnecting stream habitats, and improving stream condition so that additional high quality
habitat is available. This will help populations reach critical persistence thresholds and have a
higher likelihood of surviving disturbances, such as floods, drought, and wildfire that are
associated with climate change.

Project Tasks. Management of non-native species will be a primary concern. Introduced
rainbow trout, which would hybridize with native cutthroat, would likely need to be eliminated.
The range of three existing populations of native cutthroat trout in the watershed need to be
extended downstream and reconnected by removing existing barriers such as small irrigation
diversions and impassable culverts. At the downstream end of the watershed, some sort of
instream barrier would be required to separate native from non-native species. Restoration of
riparian areas and improved livestock management would be the focus on private-owned lands.
This would require fencing, changes in timing of livestock use, and development of off-stream
watering devices. Other rare native fishes, in this case, the flannelmouth sucker, also would need
to be accommodated by management actions. In general, ecologically-sound stream restoration
should benefit all native species, but non-native species may present special management issues
that must be addressed by species-specific actions. For example, non-native white suckers have
been introduced into the Upper Green River drainage and hybridize with flannelmouth suckers.

Implementation Schedule and Costs for Target Watershed.

Step #1, Year 1. Fish and habitat inventory to more precisely define opportunities, limiting
factors, and to establish baseline conditions. Cost estimated at $30,000.

Step #2, Year 2. Project planning, coordination, and permitting. Cost estimated at $30,000

Step #3, Years 3-6. Non-native fish control. Cost estimated at $6,000/mile for 40 miles =
$240,000.

Step #4, Years 3-6. Instream barrier removal, construction, reconstruction to increase fish
habitat and/or separate from non-native species as needed. Cost estimated at $25,000/each small
barrier for 6 barriers/watershed = $150,000. Cost for constructing one to three barriers for non-
native fish control estimated at $225,000. Total cost for barrier work $375,000.

Step #5, Years 3-7. Riparian habitat improvement, which may include native species plantings,
livestock control, fencing, or other measures as needed. Cost estimated at $10,000/mile for 30
miles = $300,000.

Step #6, Years 3-7. Inchannel stream restoration, which may include placement of large wood,
root wads, or large boulders. Cost estimated at $10,000/mile for 30 miles = $300,000.

Step #7, Years 4-8. Easements/acquisition for improved land and/or water management. Cost
estimated at $350,000, but could vary greatly.



                                                17
Step #8, Years 4-8. Road closures and/or reconstruction, and culvert replacements. Cost
estimated at $160,000. Costs substantially increase if roads are hard surface and culverts are
greater than 36” diameter.

Step #9, Years 3-10. Monitoring and evaluation to determine the effectiveness of management
actions and future needs. Costs approximately $20,000/year, which would be repeated annually
for the first several years and at some lengthier, predetermined interval in subsequent years.
Total cost $160,000 for Years 3-10.

Total costs will vary substantially depending on a number of factors such as current habitat
condition, land ownership patterns, non-native species concerns, and size of the watershed to be
treated. Nonetheless, we have attempted to describe implementation actions and associated costs
for an approximately 153,000-acre watershed in the Upper Colorado River Basin. For this
example, costs are estimated at approximately $1,945,000 over the 10-year life of this project.

Implementation Barriers. Developing good working relationships with private landowners is
key to any large-scale projects undertaken in watersheds with substantial amounts of private
land. Successful partnerships may require funding or other incentives that will be attractive to
landowners so that restoration can be implemented and best management practices employed.
Scientifically, control of non-native species may present significant obstacles because of the
large number of streams and multiple species that need to be treated. Use of fish toxicants and
the potential of fish kills also may cause landowners and recreationists to have concerns about
the project. Non-native game fish may need to be removed to make way for expansion of native
species, which in the short-term could diminish fishing opportunities. Finally, any project that
requires multiple years to implement will likely test the stamina of partnerships, funding, and
overall enthusiasm.

Conservation Outcomes. By removing instream passage barriers and expanding downstream
cutthroat trout habitat, a larger more interconnected population is created that can support
migratory as well as resident life histories. These interconnected metapopulations allow fish to
find more suitable habitats and temporarily avoid areas that may be degraded by wildfire,
drought or other disturbances (Rieman and Dunham 2000). Within the Cottonwood Creek
example, 3 small, isolated populations currently exist on approximately 35 miles of stream.
There is approximately 200 stream miles of historic habitat for Colorado River cutthroat trout in
the watershed. Restoration activities that would increase streamside shading, deep pools, and
undercut banks should allow native trout to occupy the entire watershed, at least on a seasonal
basis, which would increase the population to levels far above persistence thresholds and
significantly increase resistant to climate change-driven disturbances. Stream and riparian
restoration work would also provide substantial benefits to other native fishes, amphibians, and
other riparian-dependent wildlife.




                                                18
Figure 4.  Cottonwood Creek watershed in Upper Green River Basin, Wyoming.  Remaining native trout populations 
are almost all restricted to headwaters on U.S. Forest Service lands. 




                                  Pacific Coast Salmon Watersheds:
                                         Rogue River, Oregon

Generalized Management Situation. Adapting salmon and steelhead habitat to climate change
poses significant complexities that cannot be adequately addressed in a single case study.
Salmon and steelhead are in decline across much of their range in the lower 48 states and are at
population levels that represent only a fraction of their historic abundance. Many are vulnerable
to extinction and have been listed as threatened or endangered species. Factors responsible for
these broad declines often have been described as the 4-Hs of Habitat destruction, Hatchery
influences, Harvest of already depleted stocks, and Hydropower operations. As anadromous
species, salmon and steelhead are exposed to stressors from headwater spawning streams through
rearing and adult migratory habitat to estuaries and oceans. The sheer scope of restoring salmon
and steelhead habitat is daunting with river systems stretching hundreds of miles across multiple
states, tribal, and local government jurisdictions. Some salmon-producing rivers, such as
Oregon’s Elk River, are small but exceedingly productive, have relatively few towns or cities
within their watershed, and encompass large amounts of protected public lands. Most pose more

                                                     19
complex management dilemmas, with many competing interests, often including large cities
adding additional stressors from pollution, competition for water, and varied land alterations.
While freshwater and estuarine habitats present numerous problems and confounding issues, the
ocean offers additional stress and uncertainty in a warming future, and poses many issues that
largely are beyond our management control. Thus, our focus is on issues that we can influence
directly, including protection, reconnection, and restoration of headwater streams and their
watersheds, mainstem river and valley bottom habitats, and estuaries.

Within each species, stocks of salmon and steelhead are organized under the Endangered Species
Act into Evolutionarily Significant Units (ESU), which are spread up and down the West Coast
and inland into Idaho. Each ESU typically spans numerous river systems and may be composed
of dozens of discrete stocks that share a geographic and evolutionary legacy. Major rivers, such
as the Rogue, Columbia, Salmon, and Snake, each contain numerous stocks of several species,
further complicating management prescriptions.

Geographic and Biological Setting. The Rogue River Basin in southwestern Oregon is well
known for its fisheries, agriculture, recreation, and the growing cities of Medford, Ashland, and
Grants Pass (Figure 5). The basin heads along Crater Lake National Park on the west slopes of
the Cascade Mountains before flowing west into the Rogue River Valley, then winding through
the coast range and eventually into the Pacific Ocean. Major tributaries include the Applegate
and Illinois rivers, both of which also produce runs of salmon and steelhead with the Illinois
often touted as a regional stronghold for coho salmon and winter steelhead. The Illinois River is
undammed and flows primarily north with high quality headwaters along the California-Oregon
border region and a mainstem reach noted for whitewater flows.

Like nearly every other major salmon-producing river system, the Rogue has its share of dams
on both the mainstem and tributaries. Two major dams that are impassable to anadromous fishes
exist in the basin, including William Less Dam which impounds upper reaches of the mainstem
Rogue River into Lost Creek Reservoir and Applegate Dam in the headwaters of the Applegate
River. A third major dam on Elk Creek, a tributary of the Upper Rogue that is a primary
producer of coho salmon, was partially constructed during the 1970s but never completed and its
concrete base was notched in 2008 to allow for free passage of salmon (previously, salmon were
trucked to spawning areas above the dam). Until very recently, smaller, but still significant dams
existed on the mainstem Rogue, including Savage Rapids Dam, Gold Hill Dam, and Gold Ray
Dam, all of which were built with fish passage facilities that operated with varying degrees of
success at different flows. Gold Hill Dam was removed in 2008 and Savage Rapids Dam was
removed during 2009 and plans exist to remove Gold Ray Dam in the near future. Removal of
all three dams was planned to help sustain salmon and steelhead in the Rogue River.

Two major metropolitan areas exist in the Rogue River Basin. The larger metropolitan area,
including Medford, Central Point, Phoenix, Talent, and Ashland, occurs along Bear Creek, a
tributary of the Rogue that still produces small number of Chinook, steelhead, and even an
occasional coho. Downstream of Bear Creek, the mainstem Rogue flows through Grants Pass,
the other major metropolitan area in the basin. The Rogue is a focus for fishing, jet boating, and
river rafting, but the river also serves as a major source of irrigation and municipal water
supplies. Polluted runoff from Medford and nearby cities as well as vinyards, orchards, and

                                                20
pastureland enters the Rogue, primarily via Bear Creek. Grants Pass not only adds polluted
runoff typical of municipal areas but also poses unique problems for flooding as the mainstem
river flows through the central part of town.

Western writer Zane Grey immortalized the Rogue’s large salmon runs on the Rogue in his novel
Rogue River Feud. The basin still contains substantial runs of these fish. A 1996 review of
“healthy” salmon and steelhead stocks along the West Coast included the following populations
from the Rogue Basin: Middle Rogue Fall Chinook, Upper Rogue Fall Chinook, Applegate Fall
Chinook, Lower Rogue Winter Steelhead, and Middle Rogue Winter Steelhead. Although not
included in the 1996 review, the Illinois River by virtue of some excellent remaining habitat also
supports important stocks of coho, Chinook, and steelhead. All remaining populations of coho
salmon are listed pursuant to the Endangered Species Act.

Goals and Objectives. The overall goal of this plan is to increase the resiliency and resistance of
the aquatic system to the impacts of climate change in order to protect remaining genetic, life
history and ecological diversity of salmon and steelhead in the basin. To achieve this goal, the
following actions are necessary: protecting remaining strongholds and healthy stocks, recovering
threatened coho, improving mainstem fish passage, restoring mainstem floodplains and riparian
habitats, ensuring adequate instream flows, and reducing existing sources of pollution and other
stressors. This overall goal and associated actions are general enough to be suitable, with slight
modifications, for most West Coast river systems. Most major river systems containing salmon
and/or steelhead have existing reports, recovery plans, or other management documents that
detail recovery goals and objectives specific to that system. In general, ecologically-sound
salmon and steelhead recovery plans provide a logical starting point for developing climate
change adaptation plans.

 Project Tasks. A 2008 report from American Rivers summarized the importance of tributaries
of the Rogue River to maintaining salmon and steelhead spawning habitat and in serving as
sources of cold water. Many tributaries (11 of 14 in one July 2003 survey) exhibit lower
average maximum summer temperature compared to the mainstem Rogue. This suggests several
strategies that could be important for salmon survival in the future: 1) protection of specific
tributaries as sources of cold water, 2) restoration of riparian habitat along those streams with
higher temperatures, 3) restoration of deep pools, large wood, and channel complexity to create
cool water refuges in the mainstem Rogue and Applegate Rivers, and 4) protection and, as
needed, restoration of connectivity between mainstem and coldwater tributaries so that tributary
refugia are accessible during peak temperatures.

A specific plan for preparing the Rogue River Basin for climate change was developed in 2008
through a cooperative effort of the Climate Leadership Initiative (CLI) at the University of
Oregon and the National Center for Conservation Science and Policy (NCCSP), working in
partnership with the U.S. Forest Service. The CLI/NCCSP group used climate models to project
future conditions in the Rogue River Basin and found that annual temperatures would increase,
especially in summer, total annual precipitation would remain roughly similar but seasonal
patterns are likely to shift and rising temperatures will cause snow to turn to rain at lower
elevations. Higher winter flows were predicted but also more extreme multiple-year droughts.
Wildfires were predicted to increase substantially. For aquatic systems, these changes mean

                                                21
shifts in flow regimes, increased sediment and nutrient loads, warmer summer stream
temperatures, more floods but also more drought, and increased incidence of disease for fish
populations.

The CLI/NCCSP report made three primary recommendations for adapting aquatic systems to
future climate change: restoring stream complexity and connectivity; restoring critical habitats
that support coldwater fishes including riparian areas, floodplains, tributary junctions, and north
facing streams; and management of fisheries to protect genetic and life history diversity. The
report also recommends infrastructural changes in transportation systems and cities at the
floodplain/urban and wildland/urban interfaces to respond to future flooding along the Rogue
River and wildfires in the watershed.

Implementation Schedule and Costs for Target Watershed.

Because of the relatively large size and complexity of the Rogue River Basin, the following
recommendations necessarily are broad and would need to be refined and in coordination with
numerous agencies and other partners. Nonetheless, they are likely to be indicative of the kinds
of changes that are needed. For removal of Savage Rapids Dam and Gold Ray Dam, we provide
specific costs. Otherwise, costs are only broad approximations. Also, the entire costs for
removal of Savage Rapids Dam and for providing a replacement irrigation pumping system are
included to provide a complete picture of likely costs although much of this work already has
been funded and completed.

Recommendations to protect high quality habitats: $2.95 million
   • Protect remaining strongholds: Illinois River, Elk Creek, Silver Creek, Althouse Creek,
     Indigo Creek ($150K for public land planning)
   • Protect intact floodplains and riparian systems: Sucker Creek, East Fork Illinois River
     ($1.5 million for private land protection, easements and/or acquisition)
   • Protect north facing slope forests ($1 million for private land protection)
   • Protect remaining old-growth forests ($200K for public land planning)
   • Protect major cold-water spring inputs: headwaters of Rogue ($100K for public land
     planning)

Recommendations for reconnecting and improving mainstem passage: $50-61 million
   • Remove Savage Rapids Dam: $39.5 million (costs include preliminary studies,
     environmental compliance and permitting, design and removal, purchase and
     implementation of a new water pumping station and delivery systems, and site
     restoration)
   • Remove Gold Ray Dam: $5.5 million (costs include preliminary studies, environmental
     compliance and permitting, design, and removal; plus funding for alternative water
     delivery system; and site restoration)
   • Reconstruct or replace high priority culverts for fish passage: $3-12 million (bottomless
     archway culverts are an improved design for aquatic ecosystem health and fish)
   • Increase instream flows along salmon and steelhead streams during summer and fall low
     flow periods through acquisition, easements or voluntary appropriation: $2-4 million.


                                                22
Recommendations for restoration of high priority habitats during climate change: $11.95-21.45
million
    • Restore mainstem Rogue River floodplains (e.g., City of Grants Pass): $2-4 million
    • Restore mainstem Applegate River floodplain and riparian zones: $0.5 – 1 million
    • Provide improved stream-side buffers in agricultural and urban areas: $1-2 million
    • Restore mainstem Rogue, Applegate and Illinois woody debris, channel complexity and
        deep-pool habitats: $2.5-3.5 million
    • Provide better storm-water runoff and erosion control in urban areas (Medford-Ashland,
        Grants Pass) and nearby agricultural areas: $3-6 million
    • Restore high priority mid to high elevation meadows and riparian habitats: $2-4 million
    • Encourage riparian plantings on private lands: $0.75 million for cost-share program
    • Reintroduce beavers in headwaters to assist with erosion control, water storage and
        groundwater recharge: $0.2 million

Recommendations for improved monitoring and evaluation: $2.1 million over 10 years or
$210,000 annually
   • Increase stream monitoring for aquatic invasive species, such as bass and non-native
      mollusks: $40,000/year
   • Increase monitoring and enforcement of boats and trailers for invasive aquatic plant and
      animal species: $50,000/year
   • Increase monitoring of summer water temperatures and potential for disease outbreaks in
      Rogue, Applegate and Illinois river fish populations: $40,000/year
   • Increase monitoring of pollutants entering Rogue River drainage from urban and
      agricultural areas: $40,000/year
   • Focus monitoring on tracking basin-wide water use and conservation over time:
      $40,000/year

Recommendations for land use and water use planning: $2.6 – 4.6 million
   • Develop additional policies and programs to encourage water reuse and conservation for
     agriculture and municipal uses and capture stormwater runoff from developed lands:
     $150,000
   • Adjust and update flood maps for Rogue River and primary tributaries: $100,000
   • Identify high risk developments in Rogue, Applegate and Illinois river floodplains:
     $75,000
   • Encourage future urban areas and other developments in low-risk disturbance zones
     (away from river floodplains and wildland interface areas) and the relocation of highest
     risk existing development in disturbance zones: $2-4 million
   • Develop water sharing and conservation plans for periods of drought and severe drought
     to protect most critical fishery resources: $100,000 for planning
   • Develop water budget for Rogue River Basin, including how to fit instream needs and
     current appropriations to projected supplies: $100,000 for initial planning
   • Expand public education and outreach for climate change adaptation, especially as it
     relates to riparian protection, water conservation, and floodplain development: $100,000.



                                              23
Total adaptation costs over a 10-year period for preparing aquatic habitats of the Rogue River
Basin for climate change are estimated to range from approximately $70 – 92 million.
Estimating funds needed to fully prepare the basin, including cities, emergency and health
services, agriculture, energy and jousting infrastructure, and transportation systems, for large-
scale climate change are beyond the scope of this chapter.

Implementation Barriers. The large geographic scope of salmon and steelhead rivers poses
numerous complexities and uncertainties. Habitat from headwater spawning streams to
downstream estuaries may extend for hundreds of miles and cross numerous jurisdictions.
Coordination will likely be necessary among many city, county, state and federal agencies.
Complexity often increases as you move further downstream because human infrastructure
usually increases in lower-elevation valleys. Not only will natural resources be affected by the
actions proposed herein, but also municipal, agricultural, and industrial sectors, thus
necessitating longer-term planning, permitting, and coordination than otherwise would be
needed. Many salmon and steelhead populations are protected by laws such as the Endangered
Species Act that include additional regulatory and permitting needs. Such organizational
complexity provides additional incentive to utilize already-adopted recovery or other
comprehensive management plans as the starting framework for climate change adaptation.

Conservation Outcomes. The overall goal of this plan is to retain remaining genetic, life history,
and ecological diversity of salmon and steelhead in the Rogue River Basin during a future of
rapid environmental change fueled by global warming. Mainstem Rogue River habitat and fish
passage would be improved greatly by instream restoration and removal of Savage Rapids and
Gold Ray dams. Savage Rapids Dam is widely regarded as the largest salmon killer in the basin.
Protecting and maintaining existing habitat in the Illinois River, regarded as a stronghold
tributary system, is vital and portions of headwater spawning areas currently are threatened by
encroaching human development; problems that would be abated through this plan. Conditions
in the Applegate River, another important tributary, should be restored in part. Overall, with
implementation of recommended actions, the basin will be much more resilient to floods and
prolonged drought that are likely to become more common and severe in the future.




                                                 24
Figure 5.  Upper Rogue River Basin in southwestern Oregon.  The upstream limit for anadromous fish is William J. 
Less Dam, which impounds Lost Creek Lake. 
 


Conclusions

Three case studies have been presented for adapting coldwater fishes and their habitats to climate
change. These cases include a broad range of focal species, geography, land ownership patterns,
problems, opportunities and complexities. Varied strategies are needed to protect trout and
salmon resources during a future that on the one hand is full of uncertainties but also one that is
guaranteed to provide more and varied sources of stress to existing populations than they have
experienced during the past century.

Projections for climate change impacts to trout and salmon resources describe a likely future that
not only will be warmer but also characterized by more frequent and intense flooding, wildfire,
and prolonged drought. Adaptation strategies that strategically target watershed-scale processes
and stressors are more likely to be successful than tactical approaches aimed at specific streams
or stream segments. Understanding the broader context to adaptation will be critical.

Securing adequate funding, especially at the scale necessary to adapt entire watersheds or river
basins to climate change, will be a daunting challenge. Project and policy advocates need to
remember that many actions prescribed for coldwater fishes also provide benefits to human

                                                       25
communities, particularly those that secure stream flows and provide water during drought, and
those that help protect downstream communities from floods or wildfire. Thus many actions
described in this chapter have co-benefits for aquatic resources and human communities, which
should increase potential partnerships and revenue sources.

Invasive species already pose major problems for most native fish populations and a rapidly
changing future is likely to alter aquatic habitat conditions more rapidly, often favoring “weedy”
species that prosper in warmer, degraded habitats. Monitoring strategies should be designed to
detect habitat changes and also newly invading and expanding species.

Following ecologically-sound principles of conservation biology, such as protecting the best
remaining strongholds, reconnecting fragmented habitats, and restoring valley bottoms remains
sound advice during rapid climate change. Methods that rely primarily on technological fixes
and heavy-handed mechanical treatments should be viewed with skepticism. The best
approaches to adaption are those designed to conserve remaining genetic, life history, and
ecological diversity of native trout and salmon within protected, reconnected, and restored
watersheds.

Fortunately, trout and salmon have an evolutionary history of exposure to wide ranging
conditions and an inherent resilience to change. Change is coming faster than ever for these
fishes and their watersheds, but if trout and salmon are provided with high-quality,
interconnected habitats, they are likely to provide cultural, recreational, economic, and
ecological wealth well into the future.



_______________________________________________________________________

Table 1.  The following resources were used in preparation of this chapter and are recommended for further 
reading on the principles of stream and watershed restoration during climate change. 
 
Battin, J., M.W. Wiley, M.H. Ruckelshaus, R.N. Palmer, E. Korb, K.K. Bartz, and H. Imakl.  2007.  Projected impacts of 
          climate change on salmon habitat restoration. Proceedings of the National Academy of Sciences 
          104:6720‐6725. 
 
Doppelt, B., R. Hamilton, C. Deacon Williams, and M. Koopman.  2008.  Preparing for climate change in the Rogue 
          River Basin of southwest Oregon. Climate Leadership Institute, University of Oregon, Eugene; and 
          National Center for Conservation Science and Policy, Ashland, OR. 
 
Fausch, K.D., B.E. Rieman, M.K. Young, and J.B. Dunham.  2006.  Strategies for conserving native salmonid 
          populations at risk from nonnative fish invasions: tradeoffs in using barriers to upstream movement. U.S. 
          Forest Service General Technical Report RMRS‐GTR‐174. 
 
Flebbe, P.A., L.D. Roghair, and J.L. Bruggink.  2006.  Spatial modeling to project southern Appalachian trout 
          distribution in a warmer climate. Transactions of the American Fisheries Society 135:1371‐1382. 
 
Hamlet, A.F., and D.P. Lattenmaier.  2007.  Effects of 20th century warming and climate variability on flood risk in 
          the western U.S. Water Resources Research 43:W06427. 
 

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Heyn, K.  2008.  White paper on the biological contributions of tributary streams to the wild Rogue River, Oregon.  
          American Rivers, Washington, D.C. 
 
Hoerling, M., and J. Eischeid.  2007.  Past peak water in the Southwest. Southwest Hydrology 6(1):18‐19, 35. 
 
Hudy, M., T.M., Thieling, N. Gillespie, and E.P. Smith.  2008.  Distribution, status, and land use characteristics of 
          subwatersheds within the native range of brook trout in the eastern United States. North American 
          Journal of Fisheries Management 28:1069‐1085. 
 
Leopold, L.B.  1994.  A view of the river. Harvard University Press, Cambridge, MA. 
 
Luce, C.H., and Z.A. Holden.  2009.  Declining annual streamflow distributions in the Pacific Northwest United 
          States, 1948 – 2006. Geophysical Research Letters Vol 36, L16401. 
 
McDonald, D.B., T.L. Parchman, M.R. Bower, W.A. Hubert, and F.J. Rahel.  2008.  An introduced and a native 
          vertebrate hybridize to form a genetic bridge to a second native species. Proceedings of the National 
          Academy of Sciences 105(31):10842‐10847. 
 
Poff, N.L., M.M. Brinson, and J.W. Day.  2002.  Aquatic ecosystems and global climate change: potential impacts on 
          inland freshwater and coastal wetland ecosystems in the United States. Pew Center on Global Climate 
          Change, Arlington, VA.  
 
Rahel, F.J., and J.D. Olden.  2008.  Assessing the effects of climate change on aquatic invasive species. Conservation 
          Biology 22(3):521‐533.   
 
Rieman, B.E., D. Isaak, S. Adams, D. Horan, D. Nagel, C. Luce, and D. Myers.  2007.  Anticipated climate warming 
          effects on bull trout habitats and populations across the interior Columbia River basin. Transactions of the 
          American Fisheries Society 136:1552‐1565. 
 
Westerling, A.L., H.G. Hidalso, D.R. Cayan, and T.W. Swetnam.  2006.  Warming and earlier spring increases 
          western U.S. forest wildfire activity. Science 313:940‐943. 
 
Williams, J.E., and J. Meka Carter.  2009.  Managing native trout past peak water. Southwest Hydrology 8(2):26‐27, 
          34. 
 
Williams, J.E., C.A. Wood, and M.P. Dombeck, editors. 1997.  Watershed restoration: principles and practices. 
          American Fisheries Society, Bethesda, MD. 
 
Williams, J.E., A.L. Haak, N.G. Gillespie, H.M. Neville, and W.T. Colyer.  2007.  Healing troubled waters: preparing 
          trout and salmon habitat for a changing climate. Trout Unlimited, Arlington, VA.   
 
Williams, J.E., A.L. Haak, H.M. Neville, and W.T. Colyer.  2009.  Potential consequences of climate change to 
          persistence of cutthroat trout populations. North American Journal of Fisheries Management 29:533‐548.  
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