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8 Facilitating Recovery of Coho Salmon and Other Anadromous Fishes of the I(lamath River Restoration of anacTromous fishes to higher abundances in the I(lamath basin will require multiple interactive initiatives ancT will take many years to reach full effectiveness. This chapter emphasizes actions neeclecT for recov- ery of coho salmon; the same actions likely will benefit other species as well. RemecTial actions to be evaluatecT here inclucle restoration of tributary habitat, restoration of main-stem flows ancT habitats in the I(lamath River, removal of clams, changes in lancT use ancT water management, changes in operation of hatcheries, ancT creation of an institutional framework for fisheries management. Research ancT monitoring programs are the means by which remecTial actions shouicT be evaluatecT ancT acljustecT. RESTORATION OF TRIBUTARIES Coho salmon, spring-run Chinook salmon, ancT summer steelheacT cle- pencT heavily on tributaries to complete their life cycles ancT sustain their populations (Chapter 71. Thus, restoring large, self-sustaining runs of ana- cTromous fishes in the basin requires restoration of the tributaries to concTi- tions that favor spawning ancT rearing of anacTromous fishes. For most of the tributaries, restoring low summer temperatures probably is the most important action (Table 8-11. Removing barriers, improving physical habi- tat, ancT increasing minimum flows also are important ancT are strongly linkecT to the objective of lowering summer temperatures. Because the four main tributaries cTiffer from each other, a uniform approach to management ancT restoration in their watershecTs is unlikely to 287
288 C~ o C~ o C~ C~ C~ a~ ._ C~ ._ o C~ s~ a~ o C~ o o o o ._ 5 o s~ ~ C~ · a~ ~ ·- · (~, 5 ~E- a~ ~, ~ ._ ~ a, '~ E~ O C~ C~ Z P; ·= ¢ s~ E~ O 0 1 0 1 0 1 0 1 1 0 X X X X X X O O O O 0 1 0 1 X x 1 1 X X 1 0 1 1 0 X X X X O X O O 0 1 1 1 X 1 1 0 1 1 1 1 1 0 1 1 0 1 1 1 1 1 0 1 1 X 1 1 1 1 1 0 0 1 1 1 1 0 1 1 0 0 0 1 1 1 0 1 1 X 1 1 1 1 X X 1 x 1 0 x 1 1 1 0 O X X x 1 0 x X 0 1 0 X X X X 1 0 X X X X O O x O O x O X 1 0 1 X X X X X X X 1 1 X X X X O X x 1 1 0 X O O X O X O O X X 1 X O X X X X O O X X x 1 1 X X X X X 1 X 1 1 x x X X O s~ Ct o o Ct ~ ~ _ Ct ,- . ~ ~ . _ o ~ ~ ~ ~ ,- ~ U ~ ~ · ~ O ~ ~ · , ;, _ 'd o ~ ~ o ~ ~ ~ ~ o X ~ ~ o . ~ ~ o ~ _ ~ ~ ~ ~ ~ ~ ~ ~ . 2 ~ ~ E~ X ~ ~ ~ ~ ~ X ~ =~ V ~ ~ ~ ~ ~ ~ ~ ~ ~ 2 ~ ~ ~ ~ ~ s~ C~ bC .= ._ _ C~ ~o C~ o s~ Q 1^ .^ C~ s~ O .s O C~ Q C~ ._ X^ .^ C~ .= bC ._ C~ s~ O s~ o c~ s~ ~o ~o c~ o o .. o .- .> ¢
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 289 succeed. The following discussion outlines key issues that confront restora- tion of salmonicis in each watershed. This review is not exhaustive; it fo- cuses on the most important factors that appear to limit coho salmon anti other anaciromous species in the basin. Shasta River The Shasta River once was one of the most productive salmon streams in California (Snycler 1931' Wales 19511. It supported large runs of Chi- nook salmon, coho salmon, anti steelheacI. Over 80~000 Chinook salmon spawned in the river in the 1930s' by which time the population probably was aireacly in serious clecline as a result of habitat changes caused by placer mining anti agriculture starting in the 1850s. Snyder (1931' p.73) referred to it as early as 1931 as a "stream once famous for its trout anti salmon." The historical runs of coho salmon anti steelheacI are not known but were probably large, given the apparent quality of the habitat. An assessment of the river in the 1960s suggested that runs of coho averaged around 1,000 fish per year anti runs of steelheacI averaged around 6~000 fish per year (CDFG 19651. The productivity of the Shasta River is relatecI to its unusual hycirology anti geologic setting (Chapter 41. Unlike the Scott anti Salmon rivers, the Shasta River is clominatecI by grounc~water clis- charge, principally through numerous coicI-water springs. The heac~waters of the Shasta watershed lie primarily on the northern anti western flanks of Mt. Shasta. Rainfall anti snowmelt recharge an extensive grounc~water sys- tem that feecis the Shasta River. Historically, the river flowecI at a minimum of about 200 cfs all year. The water was coo! in summer anti, in comparison with its companion watersheds, warm in winter. The exceptional thermal stability of the Shasta macle it one of the most important tributaries for support of salmonicis in the I(lamath watershed. Today, agricultural clevelopment of the Shasta valley (principally al- falfa anti irrigated pasture) anti the construction of Dwinnell Dam (which impounds the Shastina Reservoir) have funciamentally changed the hycirol- ogy anti productivity of the Shasta River. The largest diversion of water is to the Shastina Reservoir, constructed in 1926' which loses a substantial part of its storage each year through seepage anti blocks access to about 22% of the historical salmonicI habitat. Surface diversions anti loss of spring flow to the channel because of grounc~water withcirawals have re- clucecI summer flows to about 10% of their historical rates. The low volume of flow, high contribution of warm agricultural return flows, anti loss of riparian shacling leacI to summer water temperatures that consistently ex- ceecI acute anti chronic threshoicis for salmonicis. Because of high water temperatures, the Shasta River in summer supports mainly nonsalmonicI fishes, such as the brown buliheacI anti specklecI ciace. luvenile fall-run
290 FISHES IN THE KLAMATH RIVER BASIN Chinook salmon have emigrated by summer, anti juvenile steelheacI anti coho persist mainly in the upper reaches of a few tributaries. Given its former productivity, the Shasta River has exceptional poten- tial as a restoration site for coho salmon as well as steelheacI anti Chinook salmon. Although multiple factors limit the abundance of salmonicis in the Shasta (Chapter 4), the key to their recovery is to restore enough coicI-water flow to keep the ciaily mean temperatures of the river below 20°C through- out summer. This wouicI allow juvenile salmonicis, inclucling coho, to reoc- cupy the main stem of the Shasta, where they couicI take advantage of the river's naturally high productivity. Flows must also be restored in several key tributaries (such as Parks Creek anti Big Springs) to improve their connectivity with the main river anti to provide access to spawning sites. The restoration of coicI-water flows to the Shasta River presents many clifficulties. The science behind restoration of the system, however, is relatively simple. Given the magnitude of the grounc~water recharge area that is connected to the Shasta River, there appears to be ample potential to restore coo! flows (Chapter 41. Aciclitions of coo! water to the relatively small volume of current summer flows are likely to have a substantial beneficial effect on temperature anti habitat. Moclest changes in the tim- ing anti magnitude of surface diversions anti grounc~water pumping, par- ticularly in the upper reaches of the Shasta River anti the tributaries between Dwinnell Dam anti Big Springs, wouicI have a large beneficial effect on the volume ancI temperature of water in the river cluring sum- mer. Because the thermal mass of present flows is small, the benefits of cooling the water may be limitecI to the upper reaches of the river. If new water-management programs are linkecI to programs that seek restoration of riparian zones ancI channels, however, it is very likely that a substantial portion of the Shasta River can be restored to highly productive rearing habitat for coho ancI other salmonicis. It is also appropriate to consider removal of the aging Dwinnell Dam. It loses more water to seepage than it provides for irrigation (Chapter 4), anti its removal wouicI restore flows, increase grave! recruitment, anti allow access of salmonicis to 22% of their historical habitat. Numerous stakehoicler groups anti several fecleral anti state agencies are now aciciressing habitat issues for salmonicis in the Shasta watershed. Although not as well funclecI as the Scott River programs, the Shasta River restoration efforts are making progress, particularly in riparian fencing anti management of tailwater return flow. To restore habitat effectively, these groups must clevelop methods for augmentation of the Shasta River with coo! water cluring summer. Habitat restoration efforts that fail to clear with this issue are unlikely to succeed. A feclerally organized program promoting technical review of private habitat restoration efforts couicI make such efforts more successful.
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 291 Scott River The Scott River originates in forested headwaters of the Marble, Scott, and Trinity mountains, meanders through the broad, agriculturally rich Scott valley, and then passes through the steep Scott River Canyon before joining the I(lamath River (Chapter 41. The surrounding mountains are lar~elv national forest. including the Marble Mountains Wilderness Area. ~ , , ~ in. ~ ~ . .. . . . . . . . . . . 1 he Scott diver valley Is private agricultural land, and the canyon reach below it is a state Wild and Scenic River (CDFG 1979b). The Scott River exhibits strongly seasonal flows derived from numerous tributaries that drain the western and southern edges of the watershed. The tributaries were and are critical for spawning and rearing of coho and steelhead, and the meandering river on the valley floor was important for spawning of fall-run Chinook and Pacific lamprey. It is likely that in all but the most severe drought years the main stem originally provided important and productive habitat for juvenile salmonids, including coho, throughout the summer, especially in the sloughs and pools of the numerous beaver dams that once were characteristic of the streams on the valley floor (CDFG 1979b). The Scott River is still an important spawning area for salmonids, as indicated by the annual outmigrant trapping by the California Department of Fish and Game (e.g., Chesney 20021. Numbers of fish are severely dimin- ished, however, and habitat is poor for one or more stages of the life history of all anadromous salmonids (CDFG 1979b). The decline in habitat for salmonids in the watershed has multiple, linked causes (summary in Chap- ter 41. In the forested western and southern margins of the watershed, intense logging and associated road building on highly erosive soils has produced high sediment yields. Tributaries draining that portion of the watershed have been degraded by deposition of fine sediments. In the lower portion of the tributaries, extensive diversions for irrigation remove water from streams during summer. In the valley, grazing and farming have re- duced riparian cover on tributaries and on the main stem. In addition, historical placer mining in the main stem and some tributaries has severely degraded spawning habitat, and has formed migration barriers during low- flow years. The most important effect on salmonid habitat is associated with high water demand for alfalfa and irrigated pasture. Surface diversions and groundwater pumping lead to extensive low-flow and no-flow condi- tions during summer on the main stem and the lower tributaries. Increased reliance on irrigation wells since the 1970s and changes in cropping pat- terns appear to be the cause of declining flows between late summer and 1 1- 1 1 T 1~1 1 1 1 · 1 1 · 1 1 · · · - early tall. Low flows reduce or degrade rearing habitat and limit migration during fall. Low-flow conditions on the Scott also are accompanied by poor water quality (Chapter 41. The low volume of water in the river, coupled with the accrual of tailwater return flows, leads to high summer tempera-
292 FISHES IN THE KLAMATH RIVER BASIN tures. Typical maximum weekly average temperatures are well above acute or chronic threshoicis for salmon from summer into early fall. Despite wiclespreacI clecline in suitability of habitat, the Scott River retains high potential for becoming once again a major producer of anaciro- mous fishes, especially coho salmon. The lower reaches of the tributaries on the west sicle of the basin, ancI the south ancI east forks, are still used extensively by coho ancI steelheacI despite consiclerable clegraciation of the habitat. In aciclition to continuing efforts to recluce sedimentation ancI re- store riparian vegetation cover in the streams, the key to restoring coho ancI other salmonicis is to improve access of fish to the upper basin tributaries ancI to enhance coicI-water flows. Improving access will require aciclitional screening of diversions ancI removal of blockages but also will require more aggressive management of acljuclicatecI surface diversions anti grounc~water to maintain sufficient flows for fish passage. Restoration of habitat for salmonicis on the main stem of the Scott River also remains a consiclerable challenge. Low flows ancI associated high temperatures have the greatest effect on fall-run Chinook ancI lamprey but may also affect coho, particu- larly cluring ciry falls. High water temperatures ancI loss of riparian vegeta- tion probably have eliminatecI hoicling ancI rearing habitat for coho in the main stem. Restoring summer anti fall conditions suitable for coho in the main stem will require careful ancI creative management of existing surface- water ancI grounc~water resources in the Scott River valley. Water leasing anti conjunctive use of grounc~water anti surface water may be the only means of reducing diversions anti grounc~water pumping cluring critical low-flow periods. Multiple stakehoicler groups ancI the local Resource Conservation Dis- trict in the Scott valley have concluctecI a number of well-funclecI efforts to restore habitat in the Scott watershed. Cooperation between these groups ancI the state ancI fecleral agencies that support them appears to be the most effective way of restoring habitat in the basin. To ciate, however, the groups have not attempted to resolve the most important but intractable issue: increasing the amounts of coicI water entering the tributaries anti the main stem. Salmon River The Salmon River has a steep gradient, is largely forested, ancI lacks broacI alluvial valleys. About 98% of the watershed is in fecleral ownership, ancI more than 48% is clesignatecI as wilclerness. The main stem, forks, ancI Wooley Creek are clesignatecI WilcI ancI Scenic Rivers (CDFG 1979a). Wooley Creek is in nearly pristine condition, which is unique in the I(la- math watershed. Most strikingly, the Salmon River is free of clams ancI is not subject to clepletion of flow by diversions.
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 293 The Salmon River watershed contains about 140 mi of channel suitable for spawning and rearing of fall-run Chinook salmon and 100 mi of steel- heaa and coho habitat (CDFG 1979a). Other fishes in the community include spring-run Chinook salmon and summer steelhead, which, like coho salmon, require deep pools and cola water throughout the summer. The principal habitat for spring-run Chinook salmon and summer steel- heaa in the Salmon River drainage today is Wooley Creek, although small numbers are also found in the forks of the Salmon River as well (Moyle et al. 1995, Moyle 2002~. Despite natural flow conditions and absence of agriculture, salmonia populations in general are low in the Salmon River, and coho salmon in particular are scarce (Olson and Dix 1993, Brown et al. 1994, Elder et al. 2002~. Records are poor, but salmonias most likely were considerably more 1 1 · 1 / _~ TO ~ ~ ~~ \ ~ 1 1 ~ · / ~ ~ ~ ~ \ · 1 1 abundant in the past (Lam Blab. Olson and L}1X (1~) estimated that only about 25% of the available spawning habitat was used by Chinook salmon and steelheaa. The causes of decline and the status of current popu- lations are not clear. A variety of natural and anthropogenic factors may suppress salmonia populations in the Salmon River. Unlike the Shasta and the Scott rivers- which have alluvial valleys that formed favorable habitat for holding, spawning and rearing of salmon the Salmon River has a bedrock channel of high gradient that limits the total amount of suitable habitat as defined by depth and velocity. The high rates of uplift in the watershed, coupled with unstable rock types, produce naturally high erosion rates that are associated principally with mass movements (CDFG 1979a). High erosion rates, which are accompanied by high sediment yields, have been acceler- atea by human activity in the last century (Elder et al. 2002~. In addition to naturally high sediment yields, the Salmon River water- shea exhibits strong seasonal variations in flow, including large winter floods and low base flow during the last half of the summer. Low-flow conditions in the summer, particularly during drought, and the scarcity of cola springs may have naturally produced sufficiently high summer tem- peratures (maximums, 20-26°C) in some tributaries and in the main stem to limit production of salmon within the basin. Thus, the Salmon River watershed, although nearly pristine, may have geologic and hydrologic characteristics that are suboptimal for salmon. Under these conditions, . . . . . . . . lumen activities t let increase sec lmentatlon or raise stream temperature in the basin could have an especially large effect on salmon and steelheaa. The first major anthropogenic disturbance to the Salmon River was placer mining and other forms of gold mining, which peaked in the basin between 1850 and 1900 but continue today on a small scale (CDFG 1979a, Chapter 41. Placer mining disturbs the channel and disrupts sediment trans- port processes that sustain spawning gravels and maintain pools. A more
294 FISHES IN THE KLAMATH RIVER BASIN important disturbance in recent years has been a combination of logging anti fires. Logging anti its associated roacI-builcling have greatly increased erosion on the steep anti fragile slopes of the watershed anti have reclucecI shacling of small tributaries, thus increasing water temperatures. Stream crossings also significantly impair tributary streams in this basin by forming barriers to migration anti local sources of erosion. Large fires may have exacerbated the effects of logging in the basin. Almost 30°/O of the basin has burned in the last 25 yr, anti most fires have occurred in the loggecI portions of the basin (Salmon River Restoration Council 20021. These catastrophic fires, couplecI with extensive logging that follows fires ("salvage logging"), have greatly increased the number of logging roacis anti increased the fre- quency of lancislicles (CDFG 1979a, Elcler et al. 20021. Elcler et al. (2002) estimated that from 1944 to l9SS about 216 mi of stream in the basin were scoured by clebris flows causecI by lancislicles. In aciclition, poaching of the vulnerable aclult summer steelheacI anti spring-run Chinook may be impor- tant in reducing their populations (West et al. 1990, Moyle et al. 19951. Factors outside the basin inclucling ocean or estuary conditions, har- vest, anti conditions on the I(lamath main stem may have reclucecI aclult populations of salmonicis in the Salmon River. Overall, however, it is likely that lancI-use activities in the Salmon River watershed have hacI the largest adverse effects on production of salmon anti steelheacI in the Salmon River basin. Because the Salmon River watershed is owned principally by the fecleral government, there has been comparatively little controversy surrounding management anti restoration efforts within the basin. A small but growing stakehoicler group is cooperating with state anti fecleral agencies anti tribal interests in the Salmon River basin. High priority has been placecI on moni- toring of salmon anti steelheacI runs, improvements in riparian habitat, management of fuels, anti assessment anti rehabilitation of logging roacis (Elcler et al. 20021. Given proper funding anti agency participation, these efforts may be sufficient to improve conditions for coho anti other salmon anti steelheacI in the watershed. Trinity River because the Trinity is the largest tributary of the I(lamath River anti enters only 43 mi upstream of the estuary, management anti investigative efforts by the agencies have regarclecI it as if it were a separate river system. The creation in 1963 of the Lewiston anti Trinity clams combined with the transbasin diversion of a significant proportion of the annual flow further enforces this impression of separation. Even so, the Trinity River flows influence water temperature anti quality in the lower I(lamath River anti its estuary.
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 295 The I(lamath River below Iron Gate Dam ancI the Trinity River have the same fish fauna, inclucling the runs of salmon, which belong to the same ESUs (Moyle 2002~. Chinook salmon, for example, have two ESUs: the Upper I(lamath ancI Trinity ESU ancI the Southern Oregon ancI California ESU, the latter of which inclucles salmon in the lower I(lamath ancI Trinity rivers. Both genetic evidence ancI marked hatchery fish demonstrate that salmon anti steelheacI from the two systems continuously mix. In aciclition, both systems have large hatcheries that produce coho salmon, Chinook salmon, ancI steelheacI. Immigrating spawning aclults ancI emigrating smolts from the Trinity River rely on lower I(lamath River water temperature ancI quality to support their success in terms of egg quality, osmoregulatory ability, anti survival. Thus, efforts to conserve coho salmon anti other cleclining fishes must take both systems into account. Data on the numbers of salmon ancI steelheacI returning each year to the Trinity River ancI its tributaries are fragmentary ancI incomplete. There is general agreement, however, that populations of the most sensitive salmo- nicis (coho, spring-run Chinook, anti summer steelheacI) have cleclinecI con- siclerably (perhaps 90°/O or more) to a few huncirecI inclivicluals of wilcI origin (Moyle et al. 1995, Moyle 2002, CDFG 2002~. Populations of winter steelheacI ancI fall-run Chinook also are much lower than they historically were, but there are few estimates before 1977. Between 1977 anti 1999, fall-run Chinook salmon escapement was estimated to range from about 7,000 to 125,000 fish; fewer than 25,000 spawners were present in 12 of 23 years (CDFG 19991. From 1992 through 1996, only about 1,900 aclult steelheacI were recorclecI in the river above the confluence with the North Fork River each year; this is only 5°/O of goals set in 1983, which were basecI on estimates of historical abundances (USFWS 19991. The Trinity River Hatchery releases large numbers of juvenile coho, steelheacI, anti fall-run Chinook each year, but its role in maintaining the present runs is not well unclerstoocI. Although the hatchery has been in operation since 1964, it has failecI to prevent the continued clecline of salmon ancI steelheacI popula- tions. In years when the numbers of returning Chinook salmon are low, percentages of hatchery Chinook in the run can be as much as 40-50%. Causes of the clecline in coho anti other anaciromous fishes are similar to those elsewhere in the I(lamath basin (USFWS 19991. Some of the most important probable causes of clecline specific to the Trinity River inclucle construction of clams anti associated regulation, enhancement of erosion associated with logging anti grazing practices, placer mining, anti hatchery operations. Construction of Lewiston anti Trinity clams in the main stem in 1963 blockecI access to over 109 mi of salmonicI spawning habitat (coicI water, goocI gravels), inclucling 59 mi of spawning habitat for Chinook salmon. The clams ancI associated water diversion also reclucecI flows clown- stream, blockecI recruitment of grave! to areas downstream of the clam, ancI
296 FISHES IN THE KLAMATH RIVER BASIN reclucecI rates of channel-forming geomorphic processes. Extensive poorly managed logging ancI roacI builcling on steep slopes with highly unstable soils, followecI by large fires, have resultecI in a high frequency of lancislicles ancI erosion that cause high sediment loacis in the river ancI its tributaries. Massive erosion triggered by the floocis of 1964 in particular resultecI in large-scale destruction of spawning ancI rearing habitat. In aciclition, exten- sive placer mining for goicI in the lath century, ancI to some extent into the 20th century, resultecI in loss of spawning ancI rearing habitat that still persists in many places. Finally, the Trinity River Hatchery has a major effect on wilcI populations of coho salmon, Chinook salmon, ancI steelheacI, given that marked hatchery fish are frequently observed spawning in the wilcI. It is possible that hatchery production is suppressing populations of wilcI fish (e.g., I(ostow et al. 2003), especially of coho salmon, but this has not been stucliecI in the Trinity basin. The South Fork Trinity River is one of the largest tributaries within the I(lamath basin. Although poorly clocumentecI, historical salmon ancI steel- heacI runs within the South Fork were very large, ancI incluclecI coho. Poor logging ancI grazing practices on unstable soils in the South Fork Trinity couplecI with highly destructive floocis in 1964, clestroyecI most spawning ancI rearing habitat within the South Fork. Although habitat conditions appear to be improving, this tributary acicis little to the overall salmon ancI steelheacI productivity of the basin. Recognition that runs of anaciromous fish in the Trinity River are declining ancI in neecI of recovery has lecI to many restoration projects throughout the basin. Friends of the Trinity River, for example, estimate that nearly $100 million was spent on restoration projects in the basin from 1983 through 2000 (FOTR 20031. The 1999 EIS/EIR on clam operations inclicatecI that reclucecI flows below Lewiston Dam, especially in spring, hacI significantly alterecI salmonicI habitat in the Trinity River. As a result, the Secretary of the Interior in December 2000 issued a Record of Decision (ROD) recognizing that long-term sustainability of the Trinity River's fish- ery resources requires rehabilitation of the river. The ROD callecI for spe- cific annual flows clesignecI to vary with water-year type ancI patterned to mimic natural variability in annual flows. The ROD also specified physical channel rehabilitation, sediment management, ancI watershed restoration efforts throughout the basin (USFWS 1999, 20001. Aciclitionally, the ROD callecI for an Adaptive Environmental Assessment ancI Management (AEAM) program, guiclecI by the Trinity Management Council, to use sound scientific principles in guiding the course for recovery in the Trinity River basin. Because of lawsuits by Central Valley water users challenging the EIS/EIR, however, the new flow regime has not yet been fully implementecI. Poor lancI-use practices ancI water diversions have reclucecI the capacity of the Trinity River to support coho salmon ancI other anaciromous fishes.
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 297 There are no quick fixes for problems that are so severe ancI pervasive. Some of the measures that couicI be taken to improve the situation for salmonicis both in the Trinity ancI the lower I(lamath River aireacly have been iclentifiecI in the ROD, ancI in sediment TMDLs for the main stem ancI the South Fork (EPA 1998, 20011. The proposed flow scheclule for the main-stem Trinity attempts to manage releases in a flexible manner that benefits aspects of the life histories of multiple species while responding to interannual variability in runoff conditions. Coho may benefit less than other species from main-stem flow alterations, however, clue to their affin- ity with smaller tributaries. Only large-scale restoration projects can reverse the adverse effects of logging, grazing, mining, ancI fires in the Trinity basin. Effective actions inclucle removal of roacis; elimination of logging, grazing, ancI off-roacI vehicle use from sensitive areas; planting ancI protection of trees to recluce erosion ancI restore riparian zones; ancI use of any other means to recluce erosion rates. Channel restoration ancI rehabilitation projects neecI to focus on restoring key geomorphic attributes of alluvial channels. These actions are callecI for by the ROD ancI are to be guiclecI by the Trinity Management Council. Given that 80% of the lancis within the Trinity basin are feclerally managed, large gains couicI be realizecI. It is unclear, however, whether these efforts will be restricted only to the areas immecliately downstream of Lewiston Dam or, more appropriately, will be appliecI throughout the en- tire watershed, inclucling the South Fork. A watershed approach is likely in the long run to be more successful than localizecI restoration. For coho salmon, physical restoration ancI protection of coicI-water sources in tribu- taries that were historically important for spawning ancI rearing are of key importance. Estimates of numbers of spawners of coho ancI other salmonicis are neeclecI as an inclex of the effectiveness of restoration efforts. The concept of numerical restoration goals, as set in 1983 ancI acloptecI by the 1999 FIR, is valicI, but shouicI be reviewed using information from such sources as the Indian fishery ancI extent of original habitat. The restoration goals must apply to fish spawning in tributaries as well as in the main stem. Goals shouicI inclucle minimum numbers (e.g., following years of poor ocean conclitions) as well as numbers for years of average conditions. The many small restoration projects in the basin shouicI be continued, but shouicI be viewed as experiments in aciaptive management that ulti- mately will demonstrate the most effective treatments for Trinity River problems. Coordination of existing projects with those outlinecI in the ROD shouicI be expanclecI. It is vital that management of the Trinity River, inclucling releases from Lewiston Dam, be viewed in the context of the entire I(lamath watershed. The two systems are inextricably linkecI anti are clepenclent upon each other
298 FISHES IN THE KLAMATH RIVER BASIN for long-term success. Efforts presently are uncler way to use enhanced flow releases from the Trinity to recluce the likelihoocI of fish kills in the lower Klamath. This represents an important step forward in cooperative man- agement for the sake of the entire basin, rather than a single component. Small Main-Stem Tributaries About 50 permanent streams, many of which are quite small, flow into the main-stem Klamath between Iron Gate Dam ancI the mouth of the Klamath. The streams formerly supported substantial runs of steelheacI, coho, ancI other anaciromous fishes (Kier Associates 19981. The watersheds of most of the tributaries have been extensively loggecI, ancI many roacis have been constructed in them. Irrigation diversions in the largest of the tributaries have reclucecI their summer flows. The status ancI trencis of fish populations in incliviclual tributaries for the most part are not well known, although Blue Creek ancI other nearby streams are being monitored by the Yurok Tribe (e.g., Gale et al. 1998, Hayden ancI Gale 19991. Most of these tributaries probably support far fewer aclult ancI juvenile anaciromous fish than they once clicI, because of changes to habitat causecI by logging, min- ing, agriculture, ancI roacI construction, ancI as a result of water diversions. Restoration of habitat, low temperatures, ancI flows in these small streams wouicI be of major benefit to tributary-spawning species especially coho salmon, steelheacI, ancI cutthroat trout ancI potentially couicI improve rear- ing conditions for juvenile salmonicis in the Klamath main stem by cooling the pools at the mouths of small tributaries. The emphasis on these restora- tion efforts shouicI be on those tributaries that have existing or potentially significant sources of coicI water. THE MAIN-STEM KLAMATH RIVER Modeling of Habitat Availability in Relation to Flow The National Marine Fisheries Service (NMFS) has sponsored habitat availability monitoring in the Klamath main stem in support of the prepara- tion of its biological opinions (NMFS 2001, 20021. The mocleling work was reported by Harcly ancI AcicIley (2001) in a document commonly referred to as the Harcly Phase II ciraft report. The NRC Committee was encouraged to consider the final version of this report, but was cautioned against excessive reliance on the ciraft report on grouncis that the final report wouicI contain more thorough mocle! calibration ancI possibly other changes that might alter the results. The NRC committee react ancI cliscussecI the ciraft Harcly Phase II re- port. The committee saw the mocleling approach as flawecI by heavy reli-
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 299 ance on analogies between habitat requirements for Chinook salmon ancI habitat requirements for coho salmon. Habitat requirements for Chinook salmon are better known, but the behavior ancI environmental require- ments of Chinook salmon differ substantially from those of coho salmon Chapter /). lo tne extent tnat tins approach Is carried torwarcI into the final report, the NRC committee's skepticism about the valiclity of the analogy wouicI also be carried forward. In aciclition, the NRC committee, as explainecI elsewhere in this chapter, conclucles that rearing of coho in the I(lamath main stem is much less important than rearing of coho in tributar- ies, which are the preferred rearing habitat of coho. Thus, the importance that can be attached to regulation of flows in the main stem is probably less, in the viewpoint of the committee, for coho than it wouicI be for Chinook, for example. Because the Harcly Phase II ciraft report cloes not clear with tributaries, the analysis in the ciraft Harcly Phase II clivergecI from the committee's analysis of the critical requirements for coho. / ~1 . A\ ~ .1 . . .1 . .1 · 1 · · 1 The committee recognizes that main-stem flow may clirectly affect the coho population at the time of downstream migration of smolts. While it is unclear whether aciclitional water wouicI favor the success of this migration, it is also clear, even in the absence of mocleling, that NMFS can argue, given the absence of ciata to the contrary, that there is some probability of benefit for the smolts to be clerivecI from minimum flows at the time of smolt migration, as expressed in the NMFS biological opinion of 2002. Adaptive management principles couicI be appliecI to this issue. Management of Flow at Iron Gate Dam In its biological opinions of 2001 ancI 2002, NMFS (2001,2002) callecI for increases in minimum flows from Upper I(lamath Lake via Iron Gate Dam for the benefit of coho salmon. NMFS reasoned that increased flows wouicI increase rearing habitat for juvenile coho salmon, thus increasing their growth ancI survival in the river. For bioenergetic ancI ecological rea- sons (Chapter 7), it is unlikely that increased summer flows wouicI benefit juvenile coho salmon. Aciclitional water wouicI likely be too warm for them (Chapter 4), ancI their principal habitat affinities cluring rearing are with the tributaries rather than the main stem. Aciclitional flows wouicI probably benefit Chinook salmon, steelheacI, Pacific lamprey, ancI other more ther- mally tolerant fishes in the river by providing them with aciclitional rearing habitat. There is limitecI flexibility for managing the temperature of releases from Iron Gate Dam. Some coo! water flows into Iron Gate Reservoir from springs ancI tributaries, but it is of little value for cooling the river in summer because of the large volume of the reservoir relative to these accre- tions. Because the creep waters of Iron Gate Reservoir store coo! (hypolim-
300 FISHES IN THE KLAMATH RIVER BASIN netic) water throughout the summer, however, it wouicI seem that the con- struction of a creep withcirawal, couplecI with selective aeration of the hy- polimnion cluring the summer, couicI make available a pool of water for cooling the I(lamath main stem below Iron Gate Dam. Unfortunately, the coo! summer water has a volume of only about 15,000-18,000 acre ft (M. Deas, Watercourse Engineering, Inc., personal communication, luly 16, 2003), which is sufficient to coo! the reservoir release for only seven to ten clays. Use of the water for cooling wouicI not provide sustained benefits for the fish, ancI also wouicI remove the source of coo! water for the Iron Gate Hatchery, which relies on the creep water of Iron Gate Reservoir for hatch- ery operations. Furthermore, information from thermal mocleling shows that introduction of coo! water wouicI provide benefits only for a relatively short distance downstream of the clam, given that summer thermal loacling of the main-stem I(lamath is high ancI that accretion of flow from tributar- . . . . . yes consists primary y o: - warm water In summer. Higher summer flows from Iron Gate Dam appear to increase mini- mum temperatures by reducing the effect of nocturnal cooling (Chapter 41. Higher flows also may raise the temperatures of the few coicI-water refuges available in the main stem, the pools into which coo! tributaries flow. luvenile salmonicis seek these pools cluring the clay but disperse at night as the water cools (M. Deas, Watercourse Engineering, Inc., personal commu- nication, November 25, 2002; unpublishecI data, USFWS). Even small clis- turbances to these pools (for example, by anglers) cause the fish to move into unfavorably warm water (M. Deas, Watercourse Engineering, Inc., personal communication, November 25, 2002), potentially harming or kill- ing them. A natural-flow paradigm now commonly referenced in fisheries management is basecI on the premise that ecosystem functions ancI pro- cesses anti the aquatic communities of rivers are affected by deviations from natural flows, inclucling specific seasonal patterns ancI specific interannual ranges of variability by season (Poff et al. 19971. In the I(lamath River, for example, the native fishes evolvecI with an annual sequence of winter pulse flows (principally from tributaries), high spring flows (from tributaries ancI the upper basin), ancI low flows in late summer ancI fall (principally from the upper basin). Base flows variecI with climatic conditions. Some years proviclecI strong winter ancI spring floocling that connected the channel with the floociplain, reclistributecI sediment, cleanecI gravel, ancI re-formecI the habitat features of the channel; other years hacI lower flows with much smaller effects. The timing of the flows ancI the ambient warming of the main-stem I(lamath occurred in synchrony with tributary conditions; salmon smolts emigrating from a tributary clicI not leave a cool, springflow condition to enter a main stem experiencing a warm, summer base-flow condition. Thus, managing stream flows in ways that reflect timing ancI duration of the unregulatecI hycirograph is a holistic approach that recog-
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 301 nines climatological reality but can still be consistent with extensive human use of water resources. Such an approach wouicI not clemancI high base flows in years of drought but couicI capitalize on years of high flow to maintain ancI restore habitat. It is also worth noting that historically the upper Klamath basin suppliecI only a portion of the flows of the lower Klamath River. Thus, increasing flows from the Scott ancI Shasta rivers wouicI not only have thermal benefits to the main stem but mimic natural sources of flow more closely. Temperature in the lower basin will likely be increasingly important as global climate change occurs (Parson et al. 20011. THE LOWERMOST KLAMATH AND OCEAN CONDITIONS The lowermost Klamath is important to coho as an entry ancI exit point for the main stem. In aciclition, any substantial change in the hycirograph at the mouth of the Klamath couicI be expected to influence conditions in the estuary. While it may be attractive to use Trinity flows to influence concli- tions in the lower Klamath River, it must not occur at the expense of Trinity River restoration goals. Within the ROD for the Trinity River EIS/EIR, watershed restoration ancI monitoring that benefits fishery resources below the confluence of the Trinity ancI the Klamath rivers may be consiclerecI for action by the Trinity Management Council. As explainecI in Chapter 4, total annual flow in the lower Klamath ancI its estuary has been alterecI only to a small clegree by water clevelopment in the upper basin, even though water clevelopment has hacI drastic effects on hycirographs in a number of heac~water areas. Thus, changes in total flow are not sufficiently large to suggest significant biological effects on the estuary strictly relatecI to amount of flow. Furthermore, fall flows, even in years of average or above average moisture, tencI to be higher than they were historically at the mouth of the Klamath (USFWS/HVT 1999, Harcly ancI AcicIley 2001), which wouicI indicate that fall migrations probably have not been impaired by flow clepletion per se. Warming of the water ancI poor water quality have greater potential significance, particularly near the mouth of the Klamath (see the section in Chapter 7 on fish mortality in 20021. Estuary ancI ocean conditions uncloubtecIly incluce variation from year to year in the strength of coho migrations. In part these variations are natural (i.e., they may be relatecI to synoptic changes such as those associ- atecI with Pacific clecacial oscillation or with shorter-term climate variability affecting ocean conclitions). In aciclition, as mentioned in Chapter 4, the estuary ancI river mouth have undergone chemical changes because of an- thropogenic influences upstream. The extent to which these factors are affecting coho populations is unknown at present, however. While favor- able ocean conditions may magnify the strengths of certain year classes, any such favorable effects shouicI not be used as a reason for reducing emphasis
302 FISHES IN THE KLAMATH RIVER BASIN on improvement of watershed conditions for coho, given that especially goocI ocean conditions inevitably alternate with poor ocean conditions (NRC 1996). REMOVAL OF DAMS Dams often have major adverse effects on native fishes, especially anaciromous fishes (Moyle 20021. There is growing national ancI interna- tional recognition that removal of some clams may provide substantial benefits to fish ancI downstream ecosystems by increasing flows, improving the flow regime, ancI providing access to upstream habitat (Heinz Center 2002, Hart ancI Poff 20021. Dams that have been removed so far in the United States primarily have been small ancI have hacI low or even negative economic value, although some larger clams have been proposed for re- moval on grouncis that the benefits of removal outweigh the value of the clams ancI the cost of removal. All clams (inclucling both large public or corporate clams ancI small private clams) ancI diversions in the lower I(lamath basin neecI to be system- atically evaluatecI for their effects on anaciromous fishes; those with strong adverse effects shouicI be investigated further for modification or removal. Specifically, Iron Gate Dam shouicI be evaluatecI for removal in conjunction with recapture of flows in lenny Creek that are now clivertecI out of the I(lamath basin to the Rogue River. Iron Gate Dam was built in 1962 to re- regulate flows from Copco Dam. Copco Dam was built in 1917 to generate power, mostly at times of peak clemancI. Water releasecI from the clam on clemancI caused major ciaily fluctuations in downstream flows that were harmful to the fish ancI other ecosystem components (Snycler 19311. Iron Gate Dam was intenclecI to allow more uniformity in the release of water. The reservoir behind the clam flooclecI about 6 mi of the I(lamath River. The flooclecI main-stem reach ancI its tributaries apparently were excellent spawning habitat for Chinook, coho, ancI steelheacI (Snycler 1931), prob- ably because of coo! water in the tributaries. To mitigate this loss, the Iron Gate Hatchery, which uses water from the reservoir, was built to provide a source of young salmon. The hatchery releases several million juvenile Chinook, coho, ancI steelheacI into the river each year (only about 70,000 per year are coho salmon; see Chapter 71. Iron Gate Reservoir supports a recreational fishery mainly for nonnative yellow perch ancI stocked rain- bow trout. There has been no systematic evaluation of the benefits ancI costs asso- ciatecI with the removal of Iron Gate Dam, but removal of the clam wouicI recapture about 6 mi of lost habitat in the main stem of the clam ancI substantial tributary habitat; the 6-ml reach couicI also have lower summer water temperatures than most of the main stem. Removal of Iron Gate Dam
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 303 wouicI require operation of Copco Dam in a more uniform manner, which wouicI result in loss of power revenues from Copco Dam. An alternative water supply also wouicI be neeclecI for the Iron Gate Hatchery. Opportuni- ties for removal of Iron Gate Dam couicI be consiclerecI in the near future uncler the Fecleral Energy Regulatory Commission (FERC) relicensing pro- cess. The current license for operation expires in 2006; a ciraft application is clue in 2003 (FERC Relicensing Number 20821. CHANGES IN OPERATION OF HATCHERIES The reason for builcling the hatcheries on the Trinity River ancI at Iron Gate Dam was to ensure that fisheries couicI be sustained at levels at least as high as they were before the construction of the clams. Despite the opera- tion of the hatcheries, commercial fisheries for I(lamath basin fishes have largely been shut clown, ancI sport fisheries have cleclinecI; the principal remaining fishery is the tribal subsistence fishery for salmon ancI sturgeon. Overall, anaciromous fish in the basin now reach only a small fraction of their historical abundance. Abundance has cleclinecI despite the release of millions of juvenile Chinook, coho, ancI steelheacI into the rivers each year by the hatcheries (Chapter 71. There is growing evidence from numerous river basins that large-scale releases of hatchery fish have an adverse effect on remaining populations of wilcI fish ancI clo not contribute as much to fisheries as generally supposed (e.g., Hilborn ancI Winton 1993, I(nucisen et al. 2000, Levin et al. 2001, Moyle 20021. Adverse effects can occur even when hatchery coho are stocked in streams ostensibly to help rebuilcI wilcI populations (Nickelson et al. 19861. The effect of the hatchery fish on populations of wilcI salmonicis in the I(lamath basin is not well unclerstoocI, but it probably is negative. For example, the release of millions of juvenile Chinook salmon every lune floocis the river with fish that are larger than the wilcI fish. The hatchery fish are likely to clisplace or stress wilcI Chinook ancI coho salmon (Rhocles ancI Quinn 19981. If food and space are not limiting factors in the river (that is, if the environment is not saturated with fish), hatchery fish wouicI not make much difference in the growth ancI survival of wilcI fish. But this is probably not the case, especially as the water warms ancI fish seek the coo! pools at the mouths of tributary streams. Furthermore, not all hatchery fish emi- grate as assumed when stocked. Some of the stocked fish may remain in the river, potentially until the following spring, through the process of resiclual- ization. Resiclualization occurs when the smoltification process stops ancI a juvenile fish reverts to the Parr stage (Viola ancI Schuck 19951. The smolti- fication process can stop when fish are exposed to temperatures beyond the physiological tolerance for smoltification. In some instances, large fractions of fish remain ancI compete with wilcI fish for limitecI habitat (Viola ancI
304 FISHES IN THE KLAMATH RIVER BASIN Schuck 19951. Resiclualization has not been stucliecI in the I(lamath basin, but its potential for harm to wilcI fish indicates that it shouicI be stucliecI. The I(lamath anti Trinity basins provide an unusual opportunity for large-scale tests of hypotheses relating the effect of hatchery operations to the welfare of wilcI salmon anti steelheacI populations. The two basins can be regarclecI as a paired system in many respects. Because both have procluc- tion hatcheries for coho, Chinook, ancI steelheacI at the top of the accessible reaches for the species, comparative manipulations of hatchery practices are possible through an aciaptive-management framework. For example, the Iron Gate Hatchery couicI be shut clown for 6-8 yr (two Chinook ancI coho life cycles) while the Trinity River Hatchery remains operational (with the requirement that all fish be marked when releasecI). Such a large-scale experiment wouicI be informative if accompanied by intensive monitoring of juvenile ancI aclult populations. An ecological risk analysis of the costs ancI benefits of hatchery programs shouicI be concluctecI (Pearsons ancI Hopley 1999), especially in relation to coho salmon. If hatchery production results in a net loss of wilcI coho salmon, hatchery operation shouicI be moclifiecI or even terminated. LAND-MANAGEMENT PRACTICES Throughout the distribution of coho salmon in the I(lamath basin, the effects of lancI-use practices on the welfare of coho must be closely exam- inecI anti, where ciamage to salmon habitat has occurred, restoration must be undertaken. Unclesirable practices from the viewpoint of the welfare of coho inclucle augmentation of suspenclecI loacI through any agricultural practices that enhance erosion, forestry that cloes not incorporate best man- agement practices, anti mining that cloes not involve strict controls on sediment mobilization or that occurs clirectly in a stream channel. Coho wouicI almost certainly benefit from regulation of grazing to an extent that involves exclusion of cattle from riparian zones ancI stream channels. The practice of flash grazing (exposure of riparian zones only for short inter- vals), while showing the appropriate intent, shouicI be reviewed for actual effectiveness in terms of environmental objectives. Complete exclusion of livestock may be necessary in many instances, at least until woocly vegeta- tion is well establishecI, anti streambank conditions may never be consistent with the presence of large numbers of cattle, even on a short-term basis. Plans to restore stream channels, while lauciable in intent, shouicI be re- viewecI by fecleral ancI state agencies for effectiveness; government shouicI assist lanclowners in finding the technically most clesirable ways of achiev- ing their restoration objectives. Review of channel ancI riparian conditions anti their linkages to lancI-use practices shouicI be incluclecI in a recovery plan for coho salmon (see Chapter 91.
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 305 CREATION OF A FRAMEWORK FOR FISH MANAGEMENT Management of fish in the lower I(lamath basin must deal with both harvest and habitat. For most of the history of the basin, regulation of harvest was the primary management tool, and it was complex in that it involved tradeoffs between ocean and river fisheries and among commer- cial, sport, and tribal fisheries (Pierce 19911. Despite harvest management, salmon and steelhead populations declined. Today, commercial fisheries are banned, and the sport and tribal subsistence fisheries are restricted. Reduced fishing pressure on wild fish populations, especially of coho sal- mon, is clearly part of the solution to restoration of the populations, but management of harvest does little good if spawning and rearing habitat is inadequate. The I(lamath basin requires habitat restoration. Numerous state and federal laws provide a basis of aquatic-habitat management and drive the policy of government agencies (Gillilan and Brown 19971. Examples of such legislation relevant to the welfare of fish in the lower I(lamath basin are as follows: · The Fish and Wildlife Coordination Act of 1934, which requires federal agencies to consult with state and federal wildlife agencies before any water development or modification project is undertaken; · The National Environmental Policy Act of 1970, which requires all federal agencies or holders of federal permits to file reports on the potential environmental effects of their actions; · The Wild and Scenic Rivers Act of 1968, which identifies rivers with special public values and prohibits construction of new dams on designated rivers; · The Clean Water Act of 1972, which promotes having the natural waterways of the United States be 'cdrinkable' swimmable, and fishable." Under this act, many streams in the I(lamath basin have been declared . . Impaired In water qua sty; · The Endangered Species Act of 1973 (ESA), which requires the des- ignation of "critical habitat" for endangered and threatened species (see Chapter 91; · The National Forest Management Act of 1976 (NFMA), which re- quires national forests to be managed to provide viable, widely distributed populations of all native vertebrates, including fish; · The Sustainable Fisheries Act of 1996 (SFA), which requires fisheries agencies to identity "essential fish habitats' (~;~) for managed species; · The Trinity River Stream Rectification Act (1980), which is intended to control erosion and deposition problems that arise from the Grass Valley Creek watershed; · The Trinity River Basin Fish and Wildlife Management Act (1984), which directed the Secretary of the Interior to develop a management pro-
306 FISHES IN THE KLAMATH RIVER BASIN gram to restore fish ancI wilcIlife populations in the Trinity basin to levels approximating those that existed immecliately before the TRD construc- t~on; · The Central Valley Project Improvement Act (1992), section 3406(b), which callecI for interim flows until the completion of the 12-yr Trinity River Flow Evaluation Stucly (USFWS/HVT 19991. The provision Congres- sionally requires the Secretary to implement recommendations resulting from the study. Collectively, these laws provide a strong mandate to protect ancI improve fish habitat in the I(lamath basin. Occasionally, they have resultecI in major shifts in lancI use or policy to favor fish. For example, the NFMA resultecI in the creation of a process that greatly alterecI management of public forest lancis in the Pacific Northwest (Thomas et al. 1993, FEMAT 19931. A number of I(lamath River tributaries have been clesignatecI "key water- shecis" through this process, indicating their importance to anaciromous fishes, ancI steps neeclecI to enhance their ability to support fish have been outlinecI. For the most part, however, the laws clo not require actions; rather, they provide for consultation ancI documentation of problems ancI can stimulate action. Their effect usually is to raise public awareness of problems ancI thus leacI to protection or improvement of habitat through legal ancI social channels or through changes in agency policies. An example of the potential of fecleral legislation to influence remeclial action without actually requiring it is the EFH provision of the SEA. Like the ESA for listecI species, the EFH provision clirects fisheries management agencies to look beyond harvest management to habitat management. The provision recognizes that fisheries can be sustained only if habitat is avail- able to support all life-history stages of the harvested species (Fletcher ancI O'Shea 20001. It cloes not mandate habitat management, but it cloes require the identification, by regional fisheries management councils, of the habitat for each species ancI of the factors aciversely affecting the habitat. The results of the identification process are presented to other fecleral agencies, which are acivisecI to consider them when they undertake activities that might affect the habitat. Implementation of the EFH is a large task, given that huncirecis of species are harvested, but virtually no funding has been proviclecI for it (Fletcher ancI O'Shea 20001. Even so, the EFH provision has been useful in calling public attention to the importance of habitat to the maintenance of fisheries. The EFH designations macle by the Pacific Fisheries Management Coun- cil are generic (PCFFA 20021. In this respect they resemble the critical- habitat designation macle by NMFS for Southern Oregon/Northern Cali- fornia Coast coho salmon, which inclucles all existing ancI historical habitat (FecI. Reg. 64 (861: 24061-24062 F199911. For the I(lamath basin, there is
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 307 only a general indication that EFH encompasses all anaciromous salmonicI habitat, present anti historical, without regard to species, with a generic description of the habitat requirements of each life-history stage of each species. Despite the lack of enforcement provisions in the EFH requirement of the SEA, it wouicI be worthwhile to designate species-specific EFH in the I(lamath basin as a means of assisting clecision-making in the many fecleral, state, ancI local agencies engaged in lancI ancI water management. Icleally, the EFH shouicI be used in setting priorities for conservation ancI restora- tion of habitat. POSSIBLE FUTURE EFFECTS OF CLIMATE CHANGE Records relevant to the hycirologic cycle in the I(lamath watershed are basecI on about 100 yr of rainfall anti runoff records. Probabilistic analyses of the records are used in planning future water-resource management anti in designing strategies for restoration of species at risk. Such use of the historical record is basecI on the assumption that the hycirologic cycle of the past is a general predictor of the hycirologic cycle of the future. The rapicI anti substantial rise in atmospheric mixing ratios of carbon clioxicle anti other greenhouse gas in the inclustrial era couicI contribute to a measurable increase in global mean temperatures (IPCC 2001, NRC 20011. Global circulation moclels (GCMs) indicate that global mean temperatures will rise over the next century anti that regional climates will be affected in variable ways (IPCC 2001, Strzepek anti Yates 20031. Regional climate change wouicI probably affect the hycirologic cycle of the I(lamath watershed (Snycler et al. 2002, I(im 2001, NAST 2001), but there appears to be no substantial effort on the part of government or private entities to plan for climate change. Planning, if it were to take place, faces two important hurcIles. Climate change apparently is assumed to be a distant possibility, to be clealt with after more immediate issues are re- solvecI. It is worthwhile to note, however, that regional climate change couicI occur over a period consiclerably shorter than the history of the I(lamath Project. A second hurcIle is that the current GCMs operate on a spatial scale that cannot resolve regional topographic features, which influ- ence climate in most parts of the West (NAST 2001, RecimoncI 20031. Multiple efforts are uncler way to clownscale the moclels so that they project regional climate change more accurately, but current GCMs are not suit- able for planning on a watershed scale. Even so, several regional moclels have sufficient spatial anti temporal resolution to allow realistic forecasts of the kincis of changes that are likely in a watershed (e.g., Snyder et al. 2002, I(im 2001, Lettenmaier et al. 1999, Lettenmaier anti Hamlet 20031; these moclels are potentially useful to resource managers even though they might not accurately quantify the magnitude anti timing of regional change.
308 FISHES IN THE KLAMATH RIVER BASIN A cletailecI mocle! of the I(lamath basin region at 25 mi resolution has been clevelopecI by Snyder et al. (20021. Use of the mocle! demonstrates three important kincis of changes in the hycirology of the I(lamath watershed that couicI occur over the next century: ( 1 ) warming, especially at high elevation in spring (April, May); (2) higher total precipitation, especially in spring; ancI (3) an increase in the ratio of rainfall to snowfall ancI large decreases in spring snowpack. The changes moclelecI by Snyder et al. (2002) ancI others have strong implications for management of water resources ancI all aquatic spe- cies, but especially salmonicis (NAST 2001, O'Neal 20021. For salmonicis, the most important potential changes inclucle alterecI timing of snowmelt, lower base flows, ancI aciclitional warming of water in summer. Large reductions in snowpack couplecI with higher precipitation wouicI increase winter runoff anti decrease spring runoff. LancI use ancI water management aireacly have shifted peak runoff (Figure 4-2), ancI climate change couicI increase the shift. Decline in spring runoff wouicI have impor- tant implications for spring migration of coho salmon ancI other salmonicis. Base flows cluring summer ancI fall wouicI most likely clecline in response to climate change because of increased evapotranspiration associated with higher temperatures ancI the concentration of annual runoff in winter. Base flows, especially in tributaries, aireacly are too low ancI wouicI clecline further. Increases in water temperature, particularly cluring summer low-flow periods wouicI probably harm coho salmon ancI anaciromous fishes in gen- eral (Chapter 71. Climate change couicI make temperature an even more urgent issue than it is now for the future of salmonicis in the I(lamath basin. The effects of climate change in the I(lamath basin wouicI probably vary spatially within the basin. For example, the WoocI River ancI the Shasta River both have heac~water ancI grounc~water recharge areas that lie at sufficiently high elevation to be more resilient than most stream reaches in the event of temperature increases ancI associated changes in precipita- tion. Conservation of cool-water sources in these ancI similar tributaries is likely to be even more critical in the future than it is now. Uncertainty in the magnitude ancI timing of climate change in the I(lamath basin ancI the uncertainty about its timing have cliscouragecI re- source managers from cleveloping comprehensive, specific strategies to cope with it. It is important that climate change be aciciressecI in the framework of aciaptive management (Chapter 10) through programs that anticipate changes that wouicI accompany warming. CONCLUSIONS Conditions in tributary waters are of paramount importance for rear- ing of coho salmon, as is also the case for spring-run Chinook salmon ancI
RECOVERY OF COHO SALMON AND OTHER ANADROMOUS FISHES 309 summer steelheacI, which is in contrast to other stocks of anaciromous salmonicis, inclucling fall-run Chinook. Tributary waters inclucle both the four main tributaries anti numerous small tributaries that enter these main tributaries or enter the I(lamath main stem clirectly. Small tributaries offer exceptional potential for restoration of coho salmon. Remeclial actions intenclecI to promote the welfare of coho salmon are not uniform in type anti priority across all tributaries. The Shasta River, which probably has the single largest potential for restoration of coho salmon ancI anaciromous fish in general, shows depression of salmonicI stocks causecI by extensive diversions ancI blockage of flows at small clams as well as Dwinnell Dam; diversion of spring flows for agriculture leacling to warming of these waters cluring the critical summer months; loss of riparian vegetation; reduction of base flow through diversions ancI exces- sive pumping of grounc~water; anti possible episodes of low oxygen concen- trations. The Shasta River also shows loss of substrate characteristics con- sistent with successful spawning anti has significant channel clegraciation associated with lancI-management practices. Practices leacling to the cle- graclecI state of the Shasta inclucle timber management, grazing, agriculture, and water management. The Scott River also has high potential for restoration of coho salmon. Grounc~water flows from springs are less pronounced than for the Shasta River, but an unclesirable clegree of coo! water diversion occurs through grounc~water pumping, as well as from surface diversions. Other problems closely parallel those of the Shasta, but physical clegraciation of the main- stem channel anti lower tributaries may be even more pronounced than in the Shasta. The Salmon River cirains mainly public lancis, but nevertheless shows historical reduction of coho anti other salmon populations. Degradation of the Salmon River is primarily physical, anti is associated with inadequate forest management leacling to catastrophic fires anti logging practices, especially roacI construction anti maintenance, that leacI to high levels of erosion. In aciclition, there are some flow barriers on the Salmon River. The Trinity River, which is much larger than the other three tributaries, shows the full complex of problems founcI in the Scott anti Shasta rivers, but is especially affected by loss of habitat causecI by installation of clams anti by physical damage to channels causecI by improper lancI-management practices. Implementation of actions callecI for in the Record of Decision will promote restoration anti create a framework for adaptive management through a large, comprehensive effort, but this effort must be coorclinatecI with management of the overall I(lamath basin. Small tributaries to the four large tributaries ancI to the I(lamath main stem show a wicle array of problems ancI will require treatment by category or incliviclually for effective restoration. Emphasis on coicI
310 FISHES IN THE KLAMATH RIVER BASIN water bearing tributaries is likely to yielcI the most benefit for salmonicI restoration. While the I(lamath main stem is less important for rearing of coho than to some other anaciromous taxa on the I(lamath, a number of actions on the main stem might promote the welfare of coho. Aciclitional water cluring the smolt migration couicI enhance downstream movement, ancI couicI be tested in this respect through adaptive management procedures. In acicli- tion, removal of Iron Gate Dam ancI Dwinnell Dam couicI open new habi- tat, especially by making available tributaries that are now completely blockecI to coho. Application of computer mocleling to habitat availability on the main stem is not likely to be relevant to coho, but wouicI be relevant to other taxa, such as fall-run Chinook, that use the main stem extensively for rearing. In general, coho restoration requires increased attention to lancis ancI waters beyond the I(lamath Project. Hatchery operations may have a suppressive effect on coho salmon through predation ancI competition; it shouicI not be assumed that hatchery operations are beneficial to salmonicis in general or to coho in particular. Hatchery operations couicI be viewed as acljustable rather than static ancI thus explorecI through aciaptive management principles. Because lancI-management practices are broacIly responsible for clegra- ciation of habitat that is critical to the coho, improvement of lancI-manage- ment practices ancI restoration activities in tributary waters are the key to restoration of coho populations. Restoration will require extensive work with private parties ancI with agencies that are not now strongly involvecI in ESA actions. Restoration can succeed only through substantial technical assistance in support of the consiclerable private efforts that are now uncler way. Constant evaluation of the success of specific strategies will be impor- tant to their ultimate success. A framework for overall management of fisheries exists aireacly through interlocking fecleral statutes that require conservation ancI protection of habitat ancI fishes. The Sustainable Fisheries Act of 1996 in particular seems well suited as a mocle! for management of environmental remecliation in the I(lamath basin.