Scientific Investigations Report 2006–5230

Scientific Investigations Report 2006–5230

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Rivers, streams, and lakes in the upper Salmon River Basin (defined as the area upstream of the confluence with the Pahsimeroi River) historically provided migration corridors and significant spawning and rearing habitat for anadromous Snake River spring/summer Chinook salmon (Oncorhynchus tshawytscha), sockeye salmon (Oncorhynchus nerka), and steelhead trout (Oncorhynchus mykiss). Wild salmon and steelhead trout in the basin migrate nearly 900 mi between the mountain streams at altitudes of 7,000 ft or more where they spawn, hatch, and rear, and the Pacific Ocean where they mature to adulthood. High-elevation spawning and rearing and extensive migration represent a life-history strategy unique among Columbia River Chinook salmon and steelhead trout and may be important for long-term survival of these species.

However, anadromous fish populations in the Columbia River Basin have plummeted in the last 100 years (Chapman, 1986; Thurow, 2000; Thurow and others, 2000). This severe decline led to listing these salmon and steelhead trout stocks as endangered or threatened under the Federal Endangered Species Act (ESA) in the 1990s. Most remaining populations are severely depressed; fewer than 2 percent of drainage basins in the Columbia River Basin are classified as supporting strong, wild populations of steelhead trout or Chinook salmon (Thurow and others, 2000). In addition, at least 214 stocks of anadromous salmonids are on the decline or at risk of extinction in the Pacific Northwest and California (Nehlsen and others, 1991).

Wild salmon and steelhead trout continue to migrate into the upper Salmon River Basin and depend on available spawning and rearing habitat. Resident bull trout (Salvelinus confluentus) also inhabit many rivers and streams in the Salmon River Basin. However, human development has modified the original streamflow conditions in many streams in the basin. Summer streamflow modifications (July through September) have directly affected the quantity and quality of fish habitat and also have affected migration and (or) access to suitable spawning and rearing habitat for these fish (Munther, 1974; Scott and others, 1981). Reduced summer streamflows may decrease juvenile rearing space, resulting in poor growth and survival (Quinn, 2005).

Reduced streamflows resulting from diversions also may contribute to increased water temperatures that may be unsuitable for native salmonids in the Sawtooth National Recreation Area (SNRA; M. Moulton, U.S. Forest Service, oral commun., 2003). Stream temperatures vary both spatially, throughout a stream, and temporally, over time. Many factors, both natural and human, can affect stream temperature. Stream temperatures are controlled naturally by interactions between solar radiation, ambient air temperature, streamflow, channel geomorphology, and riparian vegetation. Stream temperature tends to increase as water travels downstream. Human activities such as removal of riparian shading and alteration of streamflow can accentuate this increased water temperature.

High water temperatures generally coincide with high ambient air temperatures and usually occur during July and August. Diversions of streamflow for agricultural purposes are at their highest and streamflows generally are at their lowest during July and August. This reduction in streamflow, coupled with high ambient air temperatures, can have severe negative effects on the distribution, health, and survival of coldwater fish species.

Most Pacific Northwest fish are ectothermic (cold blooded), and their survival depends on water temperatures that are within their optimal range. When water temperature exceeds an organism’s optimal range, the organism can experience adverse health effects such as reduced growth or increased susceptibility to disease (Coutant, 1976; Beitinger and others, 2000; McCullough and others, 2001; Sauter and others, 2001; Selong and others, 2001). Different species have unique water temperature requirements, and an individual species may have a unique water temperature requirement for each of its life stages. For example, salmonids require varying water temperatures to initiate and carry out spawning, incubation, juvenile growth, and adult migration activities (Poole and others, 2001). For Chinook salmon, optimal water temperatures range from 10.0º to 17.0ºC. Adult spawning activities are triggered at water temperatures from 7.0º to 14.0ºC. Water temperatures greater than 21.0ºC, can create thermal barriers that can block adult migration to spawning grounds (Poole and others, 2001). These thermal barriers can be created by diverting streamflow for irrigation during summer when air temperatures are highest. Exposure to water temperatures greater than 21.0ºC for more than 1 week usually is fatal to adult Chinook salmon, whereas constant temperatures greater than 16.0ºC have been shown to be intolerable for bull trout (Poole and others, 2001). Ott and Maret (2003) predicted a higher probability of bull trout occurrence in streams in the Salmon River Basin where daily maximum water temperatures range from 10.0º to 15.0ºC. Bull trout passing into tributary streams to spawn in late summer may decrease when water temperatures exceed 13.0ºC and may be blocked when water temperatures exceed 18.0ºC. (J.  Dunham, U.S. Forest Service, written commun., 2004).

The Bureau of Reclamation was tasked through Reasonable and Prudent Alternative Action 149 of the National Oceanic and Atmospheric Administration (NOAA) Fisheries Biological Opinion (BiOp) of 2000 on the operation of the Federal Columbia River Power System (FCRPS) to address streamflow deficiencies in 16 priority subbasins in the Columbia River Basin (National Oceanic and Atmospheric Administration, 2000). Flow characteristic studies were done to evaluate streamflow requirements of ESA-listed fish. Results of these studies will be used to prioritize and direct cost-effective actions to improve fish habitat for ESA-listed anadromous and native fish species in the basin. These actions may include acquiring water during critical low-flow periods by leasing or modifying irrigation delivery systems to minimize out-of-stream diversions. Bureau of Reclamation considers flow characterization studies an integral part of information needed to correct flow deficiencies in the 10‑year timeframe allotted for studies in each subbasin (Spinazola, 2002).

On November 30, 2004, NOAA Fisheries issued a new BiOp for the FCRPS in response to a court order in June 2003. Action 149 objectives are restated in specific metric goals in selected subbasins for entrainment (screens), streamflow, and channel morphology (passage and complexity) in the 2004 BiOp.

Many landowners, Federal, State, and Tribal governments, and other local and private parties have completed or are completing projects to maintain, improve, and restore riparian habitat, water quality, fish passage, and other environmental conditions to protect and restore ESA-listed anadromous and native fish species in the basin (Spinazola, 2002). In addition, the Idaho Department of Fish and Game (IDFG) has completed annual redd counts and fish population assessments on the upper Salmon River and many of its major tributaries (P. Murphy, Idaho Department of Fish and Game, oral commun., 2003). The livelihoods of many people inhabiting the basin also depend on streamflows used for agricultural, domestic, commercial, municipal, industrial, recreational, and other purposes. Developing an approach to meet the needs of both people and fish rests on understanding how much streamflow is needed by each. Water quantities needed for human uses frequently can be determined from available information; however, streamflow quantities needed for ESA-listed fish habitat conservation are difficult to identify because relevant information is rarely available.

Numerous methods can be used to determine streamflow needs for fish and wildlife (Instream Flow Council, 2004), but one of the most widely used is the Instream Flow Incremental Methodology (IFIM), developed in the 1970s by the U.S. Fish and Wildlife Service (USFWS). IFIM integrates water‑supply planning concepts, analytical hydraulic engineering models, and empirically derived habitat/discharge relations to address water-use and instream-flow issues, questions concerning life-stage-specific effects on selected species, and the general well-being of aquatic biological populations. Accepted by many resource managers as an excellent process for establishing habitat/discharge relations, IFIM is the most widely used method to determine streamflow needs for fish and wildlife in the United States (Instream Flow Council, 2004).

A major component of IFIM is a collection of computer algorithms called the Physical Habitat Simulation System (PHABSIM) model. This model incorporates hydrology, stream morphology, and microhabitat preferences to create relations between streamflow and habitat availability (Bovee and others, 1998). Habitat availability is measured by the weighted usable area (WUA) index, which is the wetted area of a stream weighted by its suitability for use by an organism (expressed as the number of square feet of usable habitat per 1,000 ft of stream). PHABSIM simulates habitat/discharge relations for various species and life stages and allows quantitative habitat comparisons at different discharges.

Streamflow restoration projects developed and completed in the headwaters of the upper Salmon River will provide immediate localized benefits by restoring quality, quantity, and access to important spawning and rearing habitats. As more studies are completed in order of biological priority, and more restoration projects are implemented based on streamflow study results, streamflows needed for migration, spawning, and rearing for all fish will be systematically improved. Furthermore, restored streamflows could potentially improve spawning and rearing habitat in downstream reaches of the mainstem of the Salmon River. Additionally, if streamflows obtained from these projects are protected from downstream diversion, these benefits can be increased by improved conditions for survival throughout the Salmon River migration corridor, thereby improving long-term fish productivity.

Purpose and Scope

This report summarizes instream flow characterization results for selected streams in the upper Salmon River Basin, Idaho. Natural streamflows were characterized using continuous summer streamflow data collected upstream of diversions at selected sites. Comparisons were reported between these data and monthly discharge exceedance estimates, based on regional regression analyses.

Purposes of this report are to (1) compile, review, and analyze hydrologic and biologic data for selected streams; (2) assemble habitat suitability curves for targeted species and life stages needed to complete PHABSIM modeling and analysis; (3) provide instream flow characterization results for selected streams to identify streamflow needs from July to September to provide fish passage and support various life stages of bull trout, Chinook salmon, and steelhead trout; and (4) evaluate effects of diversions on water temperature for the selected streams.

The ultimate goal is to provide streamflow and fish habitat information to water-resource managers so informed decisions can be made to enhance instream habitat needs of ESA-listed fish species. A Web page maintained by the U.S. Geological Survey (USGS) that provides supporting data and modeling results can be accessed at

Previous Studies

Previous instream flow studies in the upper Salmon River Basin consisted of investigations for the Snake River Adjudication (SRA) process, which were funded by the Bureau of Indian Affairs (BIA) and U.S. Forest Service (USFS). The BIA funded a number of fishery studies in the Salmon River Basin that focused on development of instream flow recommendations for preservation of important fishery resources. Between 1989 and 1992, BIA contracted with EA Engineering, Science, and Technology, Inc., to develop instream flow recommendations for important fishery resources and prepared suitability criteria, conducted instream flow studies, made recommendations, and filed water right claims as part of the SRA (EA Engineering, Science, and Technology, Inc., 1989, 1991a, 1991b, 1992a, 1992b, 1992c). In cooperation with the BIA, the USGS classified Salmon River subbasins based on basin and hydrologic characteristics to assist in filing water right claims (Lipscomb, 1998). R2 Resource Consultants (2004) recently published a report about the SRA process describing methods, results, and flow recommendations for about 1,100 drainages primarily in the Salmon and Clearwater River Basins, Idaho.

Investigations by the USFS also were done by Hardy and others (1992) for protection of fishery resources on public lands. More recent (1997-98) instream flow studies also were completed by the USFS on selected streams in the upper Salmon River Basin (M. Combs, Utah State University, oral commun., 2003). These data also were collected for the SRA to evaluate minimum and maintenance streamflows for the protection of important fishery resources; however, these data were not published. The USGS completed instream flow studies on upper Salmon River Basin tributaries in 2003 and 2004 (Maret and others, 2004; 2005). In addition, instream flow studies were completed on Big Timber, Big Eightmile, Bohannon, and Hayden Creeks in the Lemhi Basin (Sutton and Morris 2004; 2005) .

Various methods have been developed to estimate streamflow needs for fish. Tennant (1976) offered one of the first methodologies for determining instream flows to protect aquatic resources. This simple approach proposes minimum stream discharges based on a percentage of mean annual discharge (MAD) that varies with the level of resource protection from poor to outstanding. Hatfield and Bruce (2000) developed equations for predicting optimum (maximum) discharge for selected salmonid life stages in western North America streams by using results from 127 PHABSIM studies. They concluded that MAD was the best predictor of optimum discharge. However, the 95-percent error estimates around the optimum predicted discharge could be substantial. NOAA Fisheries has draft protocols to estimate tributary streamflows to protect ESA-listed salmon (D. Arthaud, National Oceanic and Atmospheric Administration, written commun., 2001). These protocols offer specific guidelines based on percentages of mean monthly streamflow and PHABSIM optimum predictions.

Hydrologic studies by the USGS have provided streamflow statistics and geomorphology for streams in the Salmon River Basin. Hortness and Berenbrock (2001) developed regional regression equations that may be used to relate monthly and annual streamflow statistics to various basin characteristics (for example, basin area, basin elevation, percentage of forest cover in the basin, mean annual precipitation, and average basin slope). These equations can be useful for predicting streamflow statistics in ungaged basins. Emmett (1975) evaluated hydrology, geomorphology, and water-quality characteristics of selected streams in the Salmon River Basin.

Habitat suitability curves for depth, velocity, and substrate are available for most native fish species of the Salmon River Basin. Rubin and others (1991) empirically determined suitability curves for juvenile Chinook salmon and steelhead trout for small Salmon River tributary streams. Cochnauer and Elms-Cockrum (1986) developed suitability curves for a number of Idaho salmonid species and their life stages by using guidelines provided by Bovee and Cochnauer (1977). EA Engineering, Science, and Technology, Inc. (1991a) developed a complete set of habitat suitability curves for depth, velocity, and substrate for most native fish species in the Salmon River Basin for the BIA as part of the SRA. These curves were developed following guidelines presented by Crance (1985), which consisted of a Delphi approach. This approach involved formal meetings among fishery experts to reach a consensus on suitability curves for various species and life stages.

In 2000, the USGS, in cooperation with the Idaho Department of Environmental Quality (IDEQ), initiated studies in the Salmon River Basin to document the natural spatial and temporal variability of stream water temperature and to examine relations among stream water temperature, environmental variables, and aquatic biota in streams minimally disturbed by human activities. Results showed that temperatures in these minimally disturbed streams commonly exceeded current State and Federal stream water temperature standards.

During the summer of 2000, Donato (2002) studied the water temperature regime of 183 minimally disturbed streams in the Salmon and Clearwater River Basins to develop a predictive stream water temperature model. A major finding of this study was that water temperatures in 100 percent (119 of 119) of the streams in the Salmon River Basin failed to meet the IDEQ 9.0ºC maximum daily-average temperature (MDAT) and the 13.0ºC maximum daily-maximum temperature (MDMT) criteria for the protection of salmonid spawning. Results also showed that stream temperatures in 33 percent (39 of 119) of the streams in the upper Salmon River Basin exceeded the IDEQ 19.0ºC MDAT criterion, and temperatures in 39 percent (47 of 119) of the streams exceeded the 22.0ºC MDMT criterion for the protection of cold water biota.

In 2001, Ott and Maret (2003) studied 34 minimally disturbed streams in the Salmon River Basin to document the temperature regime, characterize the aquatic biota distribution in streams representing a gradient of temperature, and describe the relations between environmental variables and benthic invertebrate and fish assemblages. Study results showed that the maximum weekly maximum temperature (MWMT) in 100 percent (33 of 33) of the streams for which water temperature data were available exceeded the U.S. Environmental Protection Agency (USEPA) criterion of 10ºC for bull trout spawning and juvenile rearing. The MDMT in 91 percent (30 of 33) of the streams exceeded the IDEQ criterion of 13.0ºC for the protection of salmonid spawning; and the MDAT in all 33 streams exceeded the 9.0ºC criterion for the protection of salmonid spawning. Results also showed that water temperatures in 9 percent (3 of 33) of the streams exceeded the IDEQ 19.0ºC MDAT and the 22.0ºC MDMT criteria for the protection of coldwater biota.

Even though temperatures in all streams exceeded at least one water temperature criterion, Ott and Maret (2003) concluded that these same streams support populations of coldwater indicator species. They also concluded that a single stream temperature standard is difficult to apply across a broad area such as the State of Idaho because streams differ in environmental complexity and biological diversity.

Continuous summer water temperature data recorded in 2003 and streamflow relations were evaluated for Fourth of July Creek using a Stream Segment Temperature model that simulates mean and maximum daily water temperatures with changes in streamflow. Model simulation results from lower Fourth of July Creek predicted a slight increase in mean daily water temperature of 1.0ºC because of the upstream diversions removing 72 percent of the streamflow (Maret and others, 2005).

Description of Study Area

The upper Salmon River Basin (fig. 1) is in central Idaho and extends 121 mi from the headwaters on the east side of the Sawtooth Range to the confluence with the Pahsimeroi River near the town of Ellis, Idaho, draining an area of about 2,428 mi2. The basin contains large areas designated as wilderness, several national forests, and the SNRA. These features make the basin a popular destination for fishing, hiking, whitewater rafting, and other outdoor activities.

Elevation above sea level ranges from 11,815 ft at Castle Peak to 4,640 ft at the confluence of the Salmon and Pahsimeroi Rivers. Mean elevation of the basin is 7,570 ft. Climate in most of the basin is semiarid and annual precipitation averages 24 in/yr. Precipitation primarily is snow, and peak flows in streams generally result from spring snowmelt.

The upper Salmon River Basin is in the Idaho Batholith and Middle Rockies ecoregions (McGrath and others, 2001), which consist primarily of coniferous forests in upper elevations and sagebrush and grasslands in the valleys. Pine and fir predominate, covering 44 percent of the basin; rangeland covers the remaining 56 percent.

The upper Salmon River Basin geology consists primarily of metamorphic and sedimentary rocks, granite, volcanic rocks, and alluvium (King and Beikman, 1974). Much of the basin is characterized by stream channels deeply incised in bedrock and bordered by steep terrain.

Streams in the upper parts of drainage basins in the Salmon River Basin typically have high water clarity, coarse-grained substrates (cobble and boulders), high stream gradients (>0.5 percent), well-defined riffles and pools, and very sparse macrophyte growth. Designated beneficial uses for aquatic life of these study streams include cold water biota and salmonid spawning (Idaho Department of Environmental Quality, 2003). Limited water-quality sampling on small tributaries of the upper Salmon River Basin has indicated few signs of human activities (Ott and Maret, 2003). Based on IDEQ’s total maximum daily load assessments, higher elevation streams were not water-quality limited and all beneficial uses were fully supported (Idaho Department of Environmental Quality, 2003). In a few areas in the upper part of the basin, the effects of historical logging, mining, and cattle-grazing activities are noticeable. In contrast, lower elevation streams of the basin typically have lower water clarity, more fine-grained sediments, lower stream gradients, and generally denser macrophyte growth. These streams frequently are subjected to channelization, loss of riparian habitat by cattle grazing, and diversions for irrigation.

Ground water’s effect on streams in the area, especially smaller tributary streams, is important to the overall hydrology and biology. As is typical with streams in mountainous terrains, streamflow between precipitation and snowmelt periods generally is sustained by discharge from the local ground-water system. This is important because the area typically receives little precipitation during the late summer and early autumn months, which results in streamflows (baseflows) that can be directly related to local ground-water conditions. In addition, the discharge of relatively cold ground water into streams during baseflow conditions can have a significant effect on the overall water temperature of the stream.

According to SNRA biologists, the greatest effects on anadromous fish and their habitat in the upper Salmon River Basin are the effects of water diversions and related instream flow problems (Scott and others, 1981). Of about 497 diversions in the basin, about 189 are within the SNRA boundary (M. Moulton, U.S. Forest Service, written commun., 2004). However, the actual amount of water diverted is unknown. The effects of dewatering these streams include losing valuable spawning and rearing habitats; blocking access to historical spawning and rearing habitat; and disrupting the aquatic ecosystem brought about by annual recurrence of unnaturally low streamflows. Most irrigation diversions in the study area are screened to prevent loss of fish. Water for irrigation in the basin generally is diverted from July through September and, because of the high elevation (>7,000 ft), the resulting growing season is only about 80 days.

Invertebrates and fish in the Salmon River and its tributaries consist primarily of cold water species. The most common benthic invertebrate orders are Ephemeroptera (mayflies), Plecoptera (stoneflies), Trichoptera (caddisflies), and Diptera (true flies); the most common fish families are Salmonidae (trout), Cottidae (sculpins), Cyprinidae (minnows), and Catostomidae (suckers). The most common fish species in the upper Salmon River Basin include bull trout, Chinook salmon, resident rainbow (Oncorhynchus mykiss) and steelhead trout, brook trout (Salvelinus fontinalis), cutthroat trout (Oncorhynchus clarki), mountain whitefish (Prosopium williamsoni), longnose dace (Rhinichthys cataractae), and shorthead sculpin (Cottus confusus). Little historical information exists prior to irrigation on upper Salmon River tributary streams used by anadromous fish for spawning and rearing. According to IDFG, most tributary streams of the upper Salmon River offer cold water refugia for juvenile salmonid rearing when the Salmon River water temperatures are not suitable (P. Murphy, Idaho Department of Fish and Game, oral commun., 2004). In the past, the endangered sockeye salmon was found in five lakes in the upper Salmon River Basin; however, it now returns only to Redfish Lake, where active recovery efforts are in operation (National Oceanic and Atmospheric Administration, 2002).

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