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7 Habitat Loss DIMENSIONS OF THE PROBLEM Salmon habitat in freshwater is defined by physical and chemical character- istics of the environment during the portion of the life cycle spent in streams, lakes, or estuaries. It is generally taken to include Water quality: temperature, dissolved oxygen, turbidity, nutrients, and environmental contaminants. Properties of flow: velocity, turbulence, and discharge. Geological and topographic features of the stream and its valley: width and depth, streambed roughness, particle size composition, riffle and pool fre- quency, and floodplain characteristics. Cover: shading, interstitial hiding spaces, undercut banks and ledges, woody debris and aquatic vegetation. For many of those features, streamside vegetation plays an important direct and indirect role in affecting local habitat characteristics. Some biotic compo- nents of the environment are influenced by physical habitat conditions, including prey, predators, competitors, and pathogens. In this report, altered habitat is habitat that has been changed by human activity but is still accessible to salmon; lost habitat is habitat that used to be accessible but is no longer. Habitat alteration and loss that lead to reduced salmon production can occur when either of two conditions exists: anthropo- genic perturbations transform freshwater spawning or rearing habitat to an un 164

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HABITAT LOSS 165 natural or otherwise unproductive state or human intervention prevents natural disturbances from creating or maintaining habitat that is important for salmon production. Although most anthropogenic changes in habitat result in impair- ment of the productivity of aquatic ecosystems (Reice et al. l990J, some lead to increased production by improving survival or growth of one or more life-history phases. And some types of alterations do not directly affect salmon habitat but cause changes in the species composition of the aquatic community that might or might not be favorable to salmon (Reeves et al. 1987) or shift conditions from those favorable to one salmon species to those favorable to another (Lichatowich 19893. The important point is that habitat can be altered by the direct effects of human perturbations and by human prevention of natural disturbances (Sousa 1984, Wissmar and Swanson 1990~. Either can impair salmon production, espe- cially when its spatial or temporal scale differs fundamentally from that of the natural disturbance regime of an area. Habitat alterations can have positive or negative outcomes that are often difficult to predict. For example, removal of streamside vegetation, a frequent consequence of human alteration of riparian zones, results in increases in solar radiation and water temperature. Higher light levels and warmer water can promote algal growth (Gregory et al. 1987), which leads to increased invertebrate production and more food for rearing salmon (Hawkins et al. 1983~. Higher light levels also tend to enhance foraging efficiency of stream-dwelling salmon (Wilzbach 19853. The resulting increased growth rates might confer improved overwinter survival and increased smell size (Holtby and Scrivener 19893. Large smelts, in turn, might be better able to escape predation in nearshore environ- ments and have higher survival rates at sea (Pearcy 19921. All those processes potentially improve productivity. However, increased temperatures have also been shown to reduce growth efficiency when food is scarce (Brett et al. 1969) and to favor competitive dominance of cyprinid fishes, such as redside shiners (Richardsonius balteatus), over salmon (Reeves et al. 19871. And outcomes can be complicated by the presence of exotic species or pathogens, which also tend to be favored by higher temperatures (Li et al. 1987~. Those processes potentially limit salmon production. Because so many physical and biological factors, of which temperature is only one, are influenced by the removal of streamside vegetation and because interactions between these factors are still poorly understood, predictions of the specific consequences for salmon of altering stream temperatures to salmon are often prone to error. Models of the impact of habitat change on salmon generally suffer from an inability to predict the consequences of interacting ecological processes (Mathur et al. 1985, Fausch et al. 19883; this is especially true when models are extrapolated to geographical regions beyond those in which their quantitative relationships were developed (Shirvell 19891. Because habitat loss is widely acknowledged to have contributed to the decline of virtually every species of Pacific salmon in western North America

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66 UPSTREAM: SALMON AND SOCIETY IN THE PACIFIC NORTHWEST (Nehlsen et al. 1991), the lack of precise knowledge of relationships between various types of habitat change and salmon populations need not be a barrier to improved environmental management. Different land uses (e.g., forestry, agri- culture, grazing, mining, and urban and industrial development' are practiced at different locations in a river basin, but they share some effects with respect to habitat alteration and loss. This chapter identifies some important types of habi- tat alteration and loss, discusses how these changes influence the functioning of aquatic ecosystems, and identifies specific consequences for salmon. NATURAL VERSUS ANTHROPOGENIC DISTURBANCES AND WATERSHED PRODUCTIVITY Natural disturbances play a crucial role in the various life-history phases of salmon. Pacific salmon evolved in freshwater environments that included a variety of natural disturbances, including seasonal high flows and floods, gla- ciers, droughts, wildfires, volcanism, landslides and debris flows, and seasonally extreme temperatures. Their adaptations to life in frequently disturbed freshwa- ter ecosystems reflect, in part, a need to cope with unusual events. Such adapta- tions include relatively high fecundity and large eggs, which permit extended intragravel residence by alevins during periods of unfavorable stream conditions; excellent swimming abilities of both juveniles and adults; occasional straying from natal streams by adults; and differentiation into locally adapted populations. Salmon with prolonged freshwater life cycles appear to be somewhat more flex- ible in their habitat requirements than those with abbreviated or lacustrine fresh- water life cycles (Miller and Brannon 1982~. For example, Reimers (1973) identified five distinct life-history strategies involving different periods of river- ine and estuarine residence in a single population of fall chinook salmon in southern Oregon (Table 7-1~. Multiple life-history strategies within populations might be an effective means of hedging against unusual events. Not all disturbances result in diminished salmon production. Some cause short-term population declines but ultimately lead to increased productivity con- currently with habitat and trophic recovery (Gregory et al. 1987, Schlosser 1991~. Natural disturbances can alter habitat in ways that stimulate salmon production and maintain environmental heterogeneity (Neiman et al. 19921. Wildfires and some types of soil disturbances increase nutrient availability and so enhance primary production (Walstad et al. 1990~. Floods entrain particulate organic matter and both large and small woody debris from riparian zones. High flows cleanse spawning gravel of fine sediment and scour new pools. Wildfires open forest canopies, provide large woody debris, and create opportunities for early successional plant communities in riparian zones (Agee 19931. Windstorms and windthrow provide recruitment of large woody debris and increase the complex- ity of local habitats. Disturbances of many types increase the transport of nutri- ents. organic matter, and large woody debris to estuaries (Sibert 1979, Simenstad

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HABITAT LOSS TABLE 7-1 Major Variations in Fall Chinook Salmon Life Histories in Sixes Rivera 167 Life-History Variation Description 1 2 3 4 Emerge from gravel? move directly downstream through main river and estuary and into ocean within few weeks. Emerge from gravel, move into main river (or possibly stay in tributaries) for rearing until early summer, move into estuary for short period, and finally move into ocean before period of high productivity in estuary during late summer and autumn. Emerge from gravel, move into main river (or possibly stay in tributaries) for rearing until early summer, move into estuary for extended rearing, and finally enter ocean after experiencing improved growth in estuary during late summer and autumn. Emerge from gravel, stay in tributary streams (or, rarely, in main river) until autumn rains, and then move directly to ocean. Emerge from ravel; stay in tributary streams (or, rarely, in main river) through summer, autumn, and winter, and then enter ocean during next . . spring as yearlings. aA coastal Oregon stream. Source: Reimers 1973. et al. 19821. All of those processes are important to maintaining fish production in aquatic ecosystems (Gregory et al. 1991) and are necessary for normal ecosys- tem functions and diverse aquatic communities (Poff and Ward 19901. Although a large natural disturbance can cause a temporary decline in salmon populations, productivity might rebound to exceed predisturbance levels for extended periods (Bisson et al. 1988~. Some types of natural disturbances that have beneficial long-term effects on salmon habitat, such as floods and wildfires, damage prop- erty and threaten lives and so are aggressively controlled and suppressed. It is therefore important to view human activity not only as a cause of habitat change, but also as potentially hindering natural disturbance patterns and recovery pro- cesses from creating and maintaining productive and diverse habitat. Productivity declines when habitat alteration and loss impair the successful completion of life-history stages in the context of a watershed's landscape, its natural disturbance regime, and its anthropogenic changes. If a salmon popula- tion exists close to the environmental tolerance limits of its species for ex- ample, at the edge of its range either geographically or with respect to riverine environmental gradients relatively minor changes in key habitat characteristics resulting from natural climatic events or from human activity can influence popu

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68 UPSTREAM: SALMON AND SOCIETY IN THE PACIFIC NORTHWEST ration viability or expression of full evolutionary potential (Table 7-2 and 7-3~. Many of the known extinctions of salmon populations over the last century have occurred near the edges of geographical ranges (Nehlsen et al. 1991, The Wilder- ness Society 1993), and many of these have apparently been caused or accentu- ated by human-related habitat losses. Understanding the effects of habitat alter- ation must include considering changes in the context of an area's natural disturbance regime (Table 7-2J. Habitat disturbances can be "cumulative" in the sense that different factors acting sequentially or concurrently can limit population size or growth during different phases of freshwater and estuarine rearing periods (Elliott 1985~. To some extent, populations can adjust to alteration in or loss of habitat in a compen- satory fashion; after a period of decreased survival, reduction in competition can lead to increased survival or growth (Chapman 19663. However, not all factors can be compensated in this manner and interactions between different types of habitat change may exacerbate the damage each would do independently (Niemi et al. 1990, Hicks et al. 1991~. Furthermore, anthropogenic changes to habitat may occur so fast that natural selection processes are unable to adjust and com- pensate. Human activities change the frequency or magnitude of disturbances (Table 7-2), and result not only in loss of or alteration in habitat but in substantial changes in natural recovery processes (see Figure 7-la). Natural disturbances large enough to have an important impact require recovery intervals that might include periods of high production followed by re-establishment of density-de- pendent regulating mechanisms and biological controls that cause a return to predisturbance levels. There have been relatively few long-term studies of stream- dwelling salmon after large natural disturbances (Hanson and Waters 1974, Wa- ters 1983, Elliott 1985, Bisson et al. 1988), but available evidence suggests that 10 years or more might pass after a large disturbance before salmon populations return to the normal range of predisturbance abundance. Frequent anthropogenic perturbations of various intensity superimposed on natural regimes of less-frequent disturbances (Table 7-2) can hinder recovery processes and prevent populations from returning to their former abundance (Fig- ure 7-11. Such perturbations gradually "ratchet" populations downward, a pat- tern typical of salmon populations in areas of progressive encroachment on ripar- ian zones or areas with chronic input of sediment (Cederholm et al. 1981~. Frequent, relatively small perturbations tend to increase the year-to-year variabil- ity of salmon populations. Hartman and Scrivener (1990) concluded that popula- tion instability was one of the most serious long-term consequences of logging for coho and chum salmon in Carnation Creek, British Columbia. Characteristic declines occur because populations do not have time to recover fully before the next large disturbance. Very large anthropogenic impacts can cause so much damage to salmon populations or their habitat that abundance declines precipitously and does not

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HABITAT LOSS 169 recover (Figure 7-11. Such changes are characteristic of extensive habitat losses that might occur, for example, if a large portion of a river system were blocked. Sockeye salmon populations in the Fraser River underwent a major crash in 1913-1914 when rockslides caused by railroad construction in the canyon at Hell's Gate blocked much of the upper river, including most of the spawning grounds. Sockeye and other salmon that used the upper Fraser River remained at critically low densities until construction of fishways in the 1930s (Ricker 19875. Damage to or loss of habitat was so great that natural recovery was precluded until the fishways were completed. Many of the stock extinctions noted by Nehlsen et al. (1991) resulted from similar very large anthropogenic perturba- tions. The spatial and temporal scales of anthropogenic habitat alterations that are imposed on salmon populations often differ in both frequency and magnitude from natural disturbance regimes. It is the natural disturbance regimes to which local populations are adapted and that have historically powered the creation of new, productive habitat: These characteristics must be retained or replicated if freshwater salmon habitat is to be sustained (Hill et al. 19913. SEDIMENTATION Sediment can enter watercourses by various mechanisms, and inputs can be chronic or episodic. Mobilization of soil particles through surface and gully erosion delivers small particles (fine sediment) to the stream network. Surface erosion is normally associated with precipitation but can occur chronically if human activities generate continuous runoff of sediment-rich water to streams. The erosion of large volumes of hillslope material, a process termed mass ero- sion, occurs when large upper soil movements (often rapid), such as landslides, and deeply seated slope failures, such as earth slumps, deliver coarse and fine sediment, large woody debris, and fine organic matter to streams. . Both surface erosion and mass erosion are normal processes (Leopold et al. 19641; their frequency depends mostly on the geology and erosiveness of soils and underlying rock and on the intensity and duration of rainfall and snow melt (Swanson et al. 19875. Some areas have naturally high erosion rates; examples include sandstone-dominated coastal river basins in northern California and west- ern Oregon, granitic sediments in northern and central Idaho, and glacial-lacus- trine deposits in northwestern Washington. That kind of area is often among the most sensitive to erosion caused by anthropogenic perturbations, such as logging and road building (Figure 7-21. Improvements in road-construction and logging methods can reduce erosion rates. Rice (1992) documented an 80% reduction in mass erosion from forest roads and about a 40% reduction in mass erosion from logged areas in northern California due to improvements in forest practices beginning in the middle 1970s. However, the potential for continued alteration in and loss of salmon habitat

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70 UPSTREAM: SALMON AND SOCIETY IN THE PACIFIC NORTHWEST TABLE 7-2 Approximate Occurrence Rates of Different Types of Natural and Approximate Recurrence Interval (years) Type of Disturbance Natural Anthropogenic Daily to weekly precipitation and discharge patterns Seasonal precipitation and discharge; moderate storms; ice formation 0.01 - 0.1 0.001 - 0. 0.1 - 1.0 0.01 - 1.0 Major floods; storms; rain-on-snow events 10 - 100 1 - 50 Debris avalanches and debris torrents 1 Go - 1 coo 20 - 200

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HABITAT LOSS Anthropogenic Disturbances 171 Physical and Chemical Factors Influenced by the Disturbance Habitat Effects Stream discharge; channel width and depth; storage and transport of fine particulate organic matter; fine sediment transport and deposition; nutrient concentrations; water current velocity Bank-full flows; moderate channel erosion; high base-flow erosion; increased mobility of sediment and woody debris; local damming and flooding; sediment transport by anchor ice; gouging of stream bed by ice movement; reduced winter flows with extensive freezing; seasonal nutrient concentrations Inputs of sediment, organic matter and woody debris from hillslopes, riparian zones and streambanks; localized scour and fill of streambeds; lateral channel movement; streambed mobilization resulting in redistribution of coarse sediment ant! flushing of fine sediment; redistribution of large woody debris; inundation of floodplains; transport of organic matter and large woody debris t`' estuaries Large, short-term increases in sediment and large woody debris inputs; extensive channel scour; large-scale movement and redistribution of substrate, fine particulate organic matter and large woody debris; damming and obstruction of channels at the terminus of the torrent track; accelerated streambank erosion, resulting in channel widening; destruction of riparian vegetation; very large short-term increase in suspended sediment; subsequent summer temperature increases from vegetative canopy removal Minor alteration of particle sizes in spawning ~ravels; minor variations in rearing habitat; minor temperature change; altered turbidity; altered primary productivity Changes in frequencies of riffles and pools; changes in particle sizes in spawning gravels; increased channel width; flooding of side channels; removal (or sometimes addition of) cover; relocation of holding areas. In areas affected by ice: decreased water temperatures; lower primary and secondary productivity; egg dewatering or scour during anchor ice formation and breakup Changes in the frequencies of riffles and pools; formation of large log jams; burial of some spawning sites but creation of new areas suitable for spawning; increased amounts of fine particular organic matter for processing by the benthic community, resulting in increased secondary production; destruction or creation of side-channels along the floodplain; increased secondary production and cover habitat in estuaries Extensive loss of pool habitat in the torrent track; loss of spawning gravels; loss of habitat complexity along edge of stream; destruction of side-channels and other overwintering areas; creation of new cover in the terminal debris dam; creation of new spawning areas in the sediment terrace upstream from the debris dam; short-term loss of aquatic invertebrates; possible damage to gills from heavy suspended sediment load; increased primary production

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172 TABLE 7-2 Continued UPSTREAM: SALMON AND SOCIETY IN THE PACIFIC NORTHWEST Approximate Recurrence Interval (years) Natural Anthropogenic Type of Disturbance Beaver activity Major disturbances to vegetation Windthrow Wildfire Insects and disease Slumps and earthflows 5- 100 0 (removal of beavers) 100 - 500 50 - 150 (buffer strip blow-down) 100 - 750 50 - 150 (timber harvest rotation) 100 - 500 50 - 150 (timber harvest rotation) 1 00 - 1 ?0OO 50 _00

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HABITAT LOSS 173 Physical and Chemical Factors Influenced by the Disturbance Habitat effects Channel damming; obstruction and redirection of channel flow; flooding of streambanks and side-channels; entrainment of trees from riparian zone; creation of large depositional areas for fine sediment; conditions that pr~'m<.~:e anaerobic decomposition and denitrification, resulting in nutrient enrichment downstream from the pond Increased sediment delivery to channels; decreased litterfall; increased inputs of large woody debris; decreased riparian canopy; increased retention of sediment and fine organic matter; reduced litterfall Increased sediment delivery to channels; inputs of large woody debris; loss of riparian canopy and vegetative cover; short-term increase in fine particulate organic matter and nutrients; decreased litterfall; increased peak discharge; short-term increase in summer flows from reduced evapotranspiration; short-term increase in biochemical oxygen demand in stream substrate Inputs of large woody debris; loss of . . . Spartan canopy and vegetative cover; decreased litterfall; short-term increase in summer flows from reduced evapo- transpiration Low-level, long-term contributions of sediment and large woody debris to streams; partial blockage of channel; local baselevel constriction below point of entry; shifts in channel configuration; long-term source of nutrients Enhanced rearing and overwintering habitat; increased water volumes during low :llows; refugia during floods; possible blockage to upstream migration by adults and juveniles; elevated summer temperatures and lower winter temperatures; local reductions in dissolved oxygen, including areas under ice in winter; increased production of lentic invertebrates in pond; increased primary and secondary production downstream from pond Increased pool habitat; localized sedimentation; increased in-channel cover; increased summer temperatures and decreased winter temperatures; creation of eddies and alcoves along channel mat gins; increased secondary production Increased sedimentation of spawning and rearing habitat; increased pool habitat and in-channel cover' increased water volume in summer; increased summer temperatures and decreased winter temperatures; increased secondary production; reduced dissolved oxygen in spawning gravels; scour of egos and alevins in spawning gravels Increased pool habitat and in-channel cover: increased summer temperatures and decreased winter temperatures; increased water volume in summer; increased primary and secondary production Sedimentation of spawning gravels; scour of channels below point of entry; accumulation of gravels behind obstructions; possible blockage of fish migrations; increased pool habitat in coarse sediment and large woody debris depositional areas; destruction of side channels in some areas, creation of new side channels in others; long-term maintenance of aquatic productivity

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174 TABLE 7-2 Continued UPSTREAM: SALMON AND SOCIETY IN THE PACIFIC NORTHWEST Approximate Recurrence Interval (years) Type of Disturbance Natural Anthropogenic Volcanism Climate change 100- 1,000 1 ,000 - 1 00,000 1 0 - 1 00 (thermal discharges, riparian canopy removal, channelization) Source: Modified from Swanston 1991. resulting from forestry activities continues. The FEMAT report (1993) noted that federally owned forest lands within the range of the northern spotted owl contain about 180,000 km of roads, a substantial portion of which constitutes potential threats to riparian and aquatic habitats, mostly through sedimentation. An esti- mated 250,000 stream crossings are associated with the road system, and most of the crossing structures might be unable to withstand storms with a recurrence interval of less than 25 years (FEMAT 19933. Road failures often result in debris torrents in small streams and can be particularly damaging to coho, steelhead, and sea-run cutthroat habitat. Increased erosion from land use is not limited to the relatively steep forested terrain of the Pacific Northwest. For example, glacial sediment deposits in east- ern Oregon and Washington are widely farmed for the production of dryland crops. However, because extensive areas are left fallow (i.e., barren of vegetative cover) each winter, winter rainfall, particularly on frozen soils, causes much surface erosion and sediment movement to streams. Similarly, urbanization, mining, excessive grazing, and other land uses can increase sediment production well beyond background levels. Increased erosion can impair the reproductive success of salmon in several

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HABITAT LOSS TABLE 7-7 Current Requirements for Riparian Protection on State-Owned and Privately Owned Forests in California, Oregon, and Washington 193 Stream Classification Minimum Riparian Protection Zone Width Each Side `~f Stream (m) Californian Class I (fish-bearing) Class II (non-fish-bearing) Classes III & IV (no aquatic life) OregonC Type F (fish use or fish and domestic use together Type D (domestic use only) Type N (no fish or domestic use) Washingtonf Types I-III (fish-bearing) Type IV (non-fish-bearing) Type V (intermittent or ephemeral) 23-46b 15 30b None 15 30d 6-2ld o-2le 7-30g Noneh None amp to 50% of overstory and 50% of understory may be removed; exceptions for greater removal are given. bDetermined by slope steepness. CThe Oregon Rules permit timber harvest within npanan management zones as long as conifer basal requirements are met. dDifferent ripanan management area widths are specified for small, medium, and large Type F and Type D streams. eFor some small Type N streams, understory vegetation and nonmerchantable conifers must be left within 3 m of the stream. fWidths of npar~an zones along Washington's streams are determined by process called watershed analysis; some timber harvest is allowed within r~par~an management areas. "Designed to recruit, on average, 70% of historical levels of large woody debris. hVegetative buffers may be required along lower reaches of Type IV waters for temperature protection and to buffer streams from applications of forest fertilizers. Source: FEMAT 1993. ranges (e.g., Burns 19711. Unless food is extremely plentiful (a situation that rarely occurs in nutrient-poor coastal river systems', higher temperatures de- crease lower salmon growth efficiencies (Brett et al. 1969, Bisson and Davis 1976, Wurtsbaugh and Davis 1977), which must be offset by increased food production for temperature increases to be beneficial. Increased temperatures can influence the migratory behavior of spawning adults. Bjornn and Reiser (1991) cited several studies that show delays in the upstream movement of sockeye, chinook, and steelhead adults because natal streams became too warm. Berman and Quinn (1991) found that adult chinook salmon behaviorally regulated their body temperature by pausing in areas of cool

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94 UPSTREAM: SALMON AND SOCIETY IN THE PACIFIC NORTHWEST water during upstream migrations; they concluded that reduced availability of cool areas could potentially reduce spawning success. Altered thermal regimes might have an even greater effect on the production of salmon through effects on interspecific interactions between salmon and non- salmon fishes, principally competition and predation. Reeves et al. (1987) dem- onstrated that juvenile steelhead in laboratory streams were aggressively dis- placed from preferred foraging sites by juvenile redside shiners, a species of minnow, when experimentally increased temperatures became physiologically less favorable for steelhead. In a forested river system in southern Oregon, they found that the outcome of steelhead-redside shiner competition followed a ther- mal gradient in which stream warming resulted in the retreat of steelhead to higher-elevation, cooler tributaries. Many river systems in the Pacific Northwest contain a variety of introduced species that originated in warmer waters in eastern North America (Li et al. 1987), which were planted to provide a greater diversity of recreational angling opportunities. Their effects on native salmon populations are often poorly under- stood, but many species are known to prey on young salmon or compete with them for food or rearing sites at some stage in their life history. Temperature increases whether caused by riparian canopy removal, water impoundment, agricultural and urban runoff, or heated industrial discharges-create conditions favorable to many warm-water game species and might enable them to gain a competitive advantage or facilitate their predation on juvenile salmon. Altered thermal regimes can change other characteristics of habitat in streams, rivers, and estuaries by altering the structure of plant and invertebrate communities (Bisson and Davis 1976~. Aquatic plants and macroinvertebrates have specific temperature preferences. Changes in thermal regime can alter species composition in ways that might or might not be favorable to salmon production. DECREASED LARGE WOODY DEBRIS Perhaps no other structural component of the environment is as important to salmon habitat as is large woody debris, particularly in coastal watersheds. Nu- merous reviews of the biological role of large woody debris in streams in the Pacific Northwest (e.g., Harmon et al. 1986, Bisson et al. 1987, Gregory et al. l991J have concluded that woody debris plays a key role in physical habitat formation, in sediment and organic-matter storage, and in maintaining a high degree of spatial heterogeneity ("habitat complexity") in stream channels. Loss of large woody debris from streams usually diminishes habitat quality and re- duces carrying capacity for rearing salmon during all or part of the year (Hicks et al. 1991~. As with temperature, the exact manifestation of the effects of woody- debris loss on salmon is often difficult to predict. Two general trends with respect to loss of woody debris are clear. First, the

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HABITAT LOSS 195 distribution and abundance of large woody debris have been extensively altered in most river systems. Headwater streams have lost woody debris through sev- eral processes, most related to logging activity. Years of splash damming, a method of floating logs from upland logging sites to downstream mills, have scoured channels and removed much of the instream woody debris that was present. Sedell and Luchessa (1982) found that some coastal river systems in Oregon and Washington contained hundreds of active splash dams from the early to middle 1900s. In some areas without splash dams, increased frequency of landslides caused large debris torrents (Figure 7-2), scoured stream channels, and created conditions similar to those resulting from splash dams and log drives. When it became apparent that accelerated hillslope erosion had caused numerous debris torrents culminating in large, impassable logjams, fishery management agencies in the middle 1900s undertook aggressive programs of debris removal to facilitate adult salmon spawning migrations. In addition to removing the log- jams, stream-cleaning crews often removed large woody debris after logging even when there was little evidence that the debris actually constituted a migra- tion barrier (Narver 1971 J. Harvest of timber from riparian zones in coastal and western Cascade water- sheds created ideal conditions for early-successional tree species, such as red alder, which replaced late-successional conifers as the dominant form of riparian vegetation over large areas (Kauffman 1988~. Recruitment of new debris to streams from alder-dominated riparian zones was more rapid than from conifer- dominated stands, but the hardwood debris was smaller, was more prone to breakage, and decomposed faster than conifer debris (Bilby 1988), so streams in second-growth forests became progressively debris-impoverished after removal of the old-growth stand (Grette 1985, Veldhuisen 19901. Rotational harvest ages of forests on many industrial forest lands (40-60 years) have been short enough to preclude re-establishment of dominant conifers in rip arian zones (Andrus et al. 19883. The combined effects of those anthropogenic perturbations have led to a large-scale reduction in the quantity and quality of large woody debris in many forested headwater tributaries and to a substantial decline in woody debris floated downstream to lowland streams (Sedell et al. 1988~. Mainstem rivers and estuaries historically also contained great amounts of large woody debris (Gonor et al. 1988J. Some of the debris was produced in uplands and fluvially transported to depositional sites along rivers and their flood- plains, but woody debris was also recruited from riparian zones adjacent to rivers and estuaries and entered channels through natural processes of floods, wind- storms, fires, and beaver activity. Often, the lower reaches of rivers contained massive accumulations of debris that formed huge drift dams. Much of the wood in Pacific Northwest river systems was removed for navigational improvements and flood control in the late 1800s and early 1900s; for example, 368 km of the Sacramento River, 88 km of the Willamette River, and 24 km of the Chehalis River (Washington) were cleaned for river navigation from 1867 to 1912 (Sedell

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96 UPSTREAM: SALMON AND SOCIETY IN THE PACIFIC NORTHWEST et al., 19901. Rivers and estuaries containing large volumes of woody debris were characterized by spatially complex and diverse channel systems and highly productive salmon habitat, but many of these areas were lost in the early twenti- eth century. The second trend related to alteration of large woody debris abundance has been simplification of stream channels and loss of pool habitat (Figure 7-3~. Simplification occurs when loss of small-scale spatial heterogeneity leads to channel conditions characterized by uniform substrate, depth, and velocity; loss of sediment and organic-matter retention capacity; elimination of backwaters, eddies, and side channels; and loss of instream cover. In other areas of North America where habitat simplification has taken place, streams support fewer species and are less resistant to community disruption from natural disturbances (Kerr et al. 1985, Schlosser 19911. Pacific Northwest streams have fewer species than most other regions (Moyle and Herbold 1987) but have a great diversity of locally adapted populations. Streams with simplified channels usually contain fewer species than streams with structurally complex channels (Bisson et al. 1992), or they might be suitable for one age group but not multiple age groups- an important factor for salmon rearing two years or more in streams. Reeves et al. (1993) demonstrated that Oregon coastal watersheds with histories of forest management had lower salmon diversity than unmanaged watersheds. Typically, simplified channels with scarce woody debris support abundant populations of underyearling salmon but contain few yearling and older fish (Bisson and Sedell 1984, Hartman and Scrivener 1990, Reeves et al.1993~. Reduction in numbers of older salmon in simplified streams is often related to loss of pool habitat and winter cover resulting from elimination of large woody debris (Bisson et al. 1987~. Of the 43 intermediate-size tributaries with histories of forest manage- ment examined in the FEMAT report (1993) for western Oregon and Washing- ton, two-thirds had modal pool frequencies below the range of frequencies be- lieved to have existed historically (generally 25-60%~. In about half the watersheds, pools comprised less than 20% of channel areas. MIGRATION BARRIERS Dams are an important class of migration barriers and are discussed in Chap- ter 9. Many smaller barriers to migration are probably unknown. Nehlsen et al. (1991) noted that a substantial fraction of 106 stock extinctions might have resulted from migration blockages. They quoted from a story told by a Twana Indian who was born about 1865 but referred to the extinction of a sockeye run in southern Puget Sound in 1852: There were some sockeye in Mason Lake, south of Hood Canal Puget Sound area. These ran up Sherwood Creek from Allyn on Case Inlet. They'd hang around the lake till ripe, then run up the creeks from there. The Squaxon got them with a weir in Sherwood Creek. Finally a pioneer named Sherwood built

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HABITAT LOSS a little dam in the creek and stopped the fish, and they named the creek after him. 197 Many small populations might have been extirpated by similar activities in the 1800s and early 1900s. Although historical records are infrequent and usually rely on anecdotal information from people with little ability to identify salmon species, small dams probably contributed to the extinction of many local breed- ing populations, as in the case of Atlantic salmon in eastern North America. Likewise, landslides that blocked migratory routes eliminated some runs before the middle 1900s, but records were often poorly kept or lost. In many instances, nonnative stocks of salmon have been introduced into formerly blocked river systems (Johnson et al. 1991~. Rearing habitat of juvenile salmon can also be lost to blockages. Some of the most productive rearing sites in streams are located in backwaters along the edge of the channel and in side-channel areas (Sedell et al. 1984, Sedell and Beschta 19913. Highways built next to streams and rivers often disrupt access to these off-channel sites by physically isolating them from the main channel or by in- cluding culverts that are impassable for juvenile salmon. Culverts that are de- signed to pass adult salmon might create speeds that exceed the sustained swim- ming abilities of juveniles. Furniss et al. (1991) give the sustained swimming speeds of juveniles of several salmon species; they range from about 20 cm/s for juvenile coho 5 cm long to 70 crn/s for juvenile sockeye 13 cm long. Water speeds in many culverts are too great to allow juvenile passage at any time except during periods of low streamflow; in others the outfall of the culvert might be suspended too high above the water for juveniles to enter. Unscreened water diversions constitute a potential migration blockage if downstream-migrating juvenile salmon are entrained in diverted water. Nichols (1990) identified over 3,000 unscreened water diversions in Oregon, including 1,300 on coastal rivers, that potentially affected salmon-rearing streams. In addition to blocking migrations, water withdrawals potentially influence avail- able rearing habitat. Kaczynski and Palmisano (1993) reported that about 60~o of the water diversions in Oregon were for irrigation and 20% for urban uses. Palmisano et al. (1993), citing several studies by the National Marine Fisheries Service, stated that about 70% of Washington's water diversions lacked proper screening in the late 1970s and that 30% continued to be improperly screened or designed even after efforts to improve screening. WATER POLLUTION Before enactment of the federal Water Pollution Control Amendments to the Clean Water Act in the 1970s, fish kills in the United States occurred with some regularity. Dissolved-oxygen concentrations in Oregon's Willamette River in the 1940s and 1950s often dropped to anaerobic levels because of sewage and

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l9S UPSTREAM: SALMON AND SOCIETY IN THE PACIFIC NORTHWEST industrial discharges, creating an uninhabitable zone along a substantial reach of the river until nutrient discharges were controlled (Warren 19713. Anaerobic conditions often occurred in upper Grays Harbor, the estuary of Washington's Chehalis River system, during the 1920s and 1930s in response to effluents from two sulfite pulp mills, three municipal sewage-treatment plants, and agricultural runoff (Eriksen and Townsend 19401. One pulp mill, built in 1928 near the mouth of the Hoquiam River in Grays Harbor, exerted a biochemical oxygen demand of 115,000 kg/d, a load equivalent to the raw sewage produced by 1.4 million people (Seller 1989~. Water quality was degraded during low river dis- charges from May to October in Grays Harbor and was severely damaging to chinook, coho, and steelhead; but it apparently did not substantially affect chum salmon, which emigrated earlier than the other species and did not rear in the upper estuary. Pollution-abatement efforts have reduced sewage and industrial discharges over the last two decades and the upper estuary is no longer anaerobic in summer, but experimental releases of smells from hatcheries upstream have shown that a pollution block still exists in Grays Harbor and that exposure of smolts to water of poor quality has reduced seawater adaptation, increased infes- tation by a trematode parasite, lowered disease immunity, and possibly increased vulnerability to predation by birds and squawfish. Smolts in the Chehalis River system survive at roughly half the rate of smelts from a nearby, relatively unpol- luted river (Seller 19891. The case study of Grays Harbor has been well docu- mented and might be representative of the effects of water-quality degradation on salmon in lower rivers and estuaries with heavy urban and industrial develop- ment. Although the concentration of pollutants in wastewaters is now regulated more strictly than before, the volume of pollutants in water could be equal to or greater than volumes existing before water-quality laws were enacted. Servisi (1989) estimated that the volume of wastewater discharged into the Fraser River had tripled since 1965. Mining is another source of water pollution in Pacific Northwest rivers. Nelson et al. (1991), citing a study by the Environmental Protection Agency, reported that in 1961-1975 at least 10 million fish were killed nationally by mining-related water pollution, although the number of salmon included was not given. Nelson et al. (1991) provided a thorough discussion of the different types of water pollution resulting from mining activity: in western North America, metals and radionuclides from mining wastes can be highly toxic to salmon; some highly toxic metals, such as copper and zinc, are also highly synergistic- their combined effects greatly increase lethality. Furthermore, metals can "bio- accumulate" in fish tissues, causing long-term stress and posing potential health threats to people consuming the fish. Sediment can be an important byproduct of mining activity. In an Idaho tributary of the Salmon River, Konopacky et al. (1985) found that dredging for rare earths generated 500,000 m3 of sediment, which smothered important downstream spawning and rearing areas of chinook salmon and steelhead. Spaulding and Ogden (1968) estimated that hydraulic

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HABITAT LOSS 199 mining for gold in the Boise River, Idaho, generated 116.5 million kilograms of sediment in 18 months. LOSS OF REFUGES Because natural disturbances were an important part of the freshwater envi- ronment of Pacific salmon, many populations, particularly those at the edges of the range, underwent periodic expansion and contraction in response to local extinctions and periods of recolonization. That process fostered genetic diversity and versatility and enabled salmon to be resilient and locally variable (Scudder 1989~. Over the last century, many small populations have become extinct as a result of human activity (Nehlsen et al. 1991, Frissell 1993), and the geographical distribution of some species has become highly fragmented (The Wilderness Society 19931. Within the confines of a river basin, the ability of salmon to recolonize areas of local population loss, such as a third- to fourth-order tributary system, might depend on the presence of refugia (survival areas) containing high quality habitat and relatively stable populations (Sedell et al. 19901. At present, watersheds without substantial anthropogenic perturbations are limited almost solely to national parks and designated wilderness areas, and in the Pacific North- west states these are usually at elevations above the occurrence of anadromous salmon. High-quality habitat might exist in small patches within river basins that are subject to land and water management, but often habitat refugia widely dis- tributed throughout the system there are insufficient for colonization of nearby disturbed sites (Sedell et al. 19901. Concern for the continued viability of Pacific salmon on federally owned forest lands has led to the establishment of "key watersheds" in which high priority is given to protecting stream habitat (Figure 7-4) (Reeves and Sedell 1992, FEMAT 19933. Protection of habitat watersheds will be achieved by controlling erosion and by leaving large riparian buffers adjacent to both fish- bearing and non-fish-bearing streams. However, the distribution of key water- shed reserves is limited primarily to headwater drainages where national forests are located (FEMAT 19933; few are in lower river valleys and coastal lowlands. In the Pacific Northwest landscape, the latter kinds of environment lack refugia with high-quality habitat for salmon (Frissell 1993), and there seems to be little hope of future establishment of such areas without considerable public resolve and financial commitment. SUMMARY Habitat for salmon in Pacific Northwest river basins has been lost or exten- sively altered over the past 150 years. As a result of alteration and degradation of biophysical conditions, many salmon populations have been extirpated or de

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200 Key Watersheds Tier ~ Tier 2 UPSTREAM: SALMON AND SOCIETY IN THE PACIFIC NORTHWEST ? \ FIGURE 7-4 Key watersheds in the Pacific Northwest identified in the president's forest plan. The shaded area indicates the known range of the northern spotted owl (Strix occidentalis caurina). Source: FEMAT 1993.

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HABITAT LOSS 201 pleted. Although the full extent of the modifications of salmon habitat will never be known, some generalizations are possible. As a result of human development, the current condition of most river basins in California, Idaho, Oregon, and Washington is significantly different from the conditions in which salmon evolved. Stream-habitat alterations and losses asso- ciated with many types of land uses have included increased sediment loading, higher and more variable water temperatures, reduced amounts of large woody debris, reduced and simplified riparian plant communities, new barriers to migra- tions, lower streamflows during some periods and higher peak flows at other times, loss of stream-bank integrity, simplified channel structure, and reduced small-scale habitat heterogeneity. These changes have generally reduced the productivity of river basins for salmon, although some changes have occasionally increased production. Anthropogenic habitat disturbances have often resulted in simultaneous changes in a wide variety of functions, processes, and habitat characteristics. It has usually been impossible to identify which habitat changes have had the greatest effect on salmon. Human-caused disturbances have interacted with natu- ral ones: for example, effects of widespread removal of riparian vegetation, loss of ground cover, or decreased stability of hillslopes have sometimes not been manifested until after a heavy rainfall or snowfall. The simultaneous alteration of many factors had important implications for habitat rehabilitation. First, it is important to avoid attempting only to improve individual aspects of habitat (e.g., pools in streams) without addressing other aspects that might be equally degraded and are critical to salmon production. It is not enough to improve a pool in a stream, for example, if the water is too warm to support salmon. In many cases, these single-factor approaches are not effective (NRC 1992a). Second, rehabili- tating watershed processes to the extent possible given human development, including the re-establishment of riparian functions such as providing shading, organic matter, and large woody debris-is probably more effective in improving salmon habitat over the long-term than substituting artificial structures for eco- logical functions. Habitat changes caused by human activities have occurred at far different spatial and temporal scales than natural disturbances in the Pacific Northwest. These differences between anthropogenic and natural disturbance patterns have interfered with the abilities of salmon to survive and recover from changes in their habitat. Anthropogenic perturbations have been significant causes of direct mortality for juvenile and adult salmon. Examples include excessive sediment inputs, scouring of reads, creation of migration blockages, high water tempera- tures, and toxic discharges. Catastrophic habitat loss can also occur as a result of natural disturbances, but the frequency and spatial scale of natural disturbances- unlike those of many human-caused disturbances are such that salmon's behav- ioral and physiological characteristics allow their populations to be resilient. Human activities have prevented natural disturbance regimes from creating

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202 UPSTREAM: SALMON AND SOCIETYIN THE PACIFIC NORTHWEST or maintaining productive salmon habitat. In addition to imposing new distur- bance regimes, the land- and water-management actions of an increasing human population have systematically prevented natural disturbances from providing crucial raw materials for productive habitat. Examples include flood control and wildfire suppression, both of which have interfered with processes that provide woody debris and nutrients to river systems. In addition, stream processes have been altered to the extent that they cannot respond to natural disturbances in a normal manner. Rehabilitating ecologically productive watersheds will require allowing natural disturbances to occur to the greatest extent possible. Habitat alteration has changed the outcome of interactions between salmon and other species. Increased water temperatures, for example, have favored warm-water species at the expense of cold-water species such as salmon. In addition, many Pacific Northwest river basins contain nonnative fishes intro- duced from eastern North America and elsewhere, which are often better adapted to warm temperatures than salmon and which can prey on or outcompete young salmon. Some habitat alterations unfavorable for salmon have resulted from exotic animals or plants. Habitat protection-especially with respect to riparian zones has been very uneven across different types of land uses and ownerships. Overall, streams on public lands receive greater protection than those on private lands; those on forested lands often receive greater protection than those on agricultural and range lands; and streams and sloughs in urban and industrial areas have generally received the least protection. Water-quality requirements also differ according to the predominant use or according to various federal, state, and local discharge regulations. There often are large variations in the degree of protection afforded in different places within a river basin. Habitats on private and public lands are important to salmon, and rehabilitation programs that focus only on public lands will be less effective than those involving private lands as well (NRC 1995b). Therefore, cooperation between private and public landowners is important to protecting and rehabilitating habitat at a watershed scale. Development of coop- erative habitat-conservation agreements between public and private landowners and resource managers will help identify critical habitat areas in need of rehabili- tation while providing site-specific flexibility for landowners to provide different types of protection measures (see also Chapter 13 and NRC l995b). So much habitat has been lost or altered that relatively few areas of high- quality habitat remain, especially in large river valleys and in coastal lowlands- typically home to large numbers of people. Therefore, protecting and rehabilitat- ing enough habitat to provide refuges for salmon and sources for recolonization of other areas that might be improved in the future will entail operating in a context of human development in other words, ways must be developed for people and salmon to live together. Although many of the best remaining sites are in forested headwaters, nodes of good habitat are also needed in large river valleys and coastal lowlands. These sites can be identified and locally based

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HABITAT LOSS 203 protection measures can be developed. In some cases, landowner incentives can be used as a financial carrot in place of the more traditional regulatory stick. An example of such a program is King County's Waterways 2000, an aquatic conser- vation program funded from county real-estate taxes. It provides with tax reduc- tions to landowners for dedicating part of their property to riparian protection, outright purchases of important greenways and conservation easements, and pub- lic education emphasizing good stewardship of the county's streams. The initial phase of the program has already helped to protect good habitats in six important salmon watersheds in this urban area, which includes Seattle (King County Sur- face Water Management Division 19959.