Scientific Investigations Report 2006–5230
U.S. GEOLOGICAL SURVEY
Scientific Investigations Report 2006–5230
Rivers, streams, and lakes in the upper Salmon River Basin historically provided migration corridors and significant habitat for anadromous Chinook salmon, sockeye salmon, and steelhead trout. Wild salmon and steelhead in the basin migrate nearly 900 miles between the mountain streams and the Pacific Ocean. Resident bull trout also inhabit many of the rivers and streams in the basin. High-altitude spawning and rearing and extensive migrations may be very important for the long-term survival of these species.
Anadromous fish populations in the Columbia River Basin have plummeted in the last 100 years; this severe decline led to listing Chinook salmon and steelhead trout stocks as endangered or threatened under the Federal Endangered Species Act (ESA) in the 1990s. Human development has modified the original flow conditions in many streams of the upper Salmon River Basin. Summer streamflow modifications, as a result of irrigation practices, 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. Reduced streamflows resulting from diversions may contribute to increased water temperatures that may be unsuitable for native salmonids.
As a result of these ESA listings and Action 149 of the Federal Columbia River Power System Biological Opinion of 2000, the Bureau of Reclamation was tasked to conduct streamflow characterization studies in the upper Salmon River Basin to clearly define habitat requirements for effective species management and habitat restoration. These studies were done to evaluate potential fish habitat improvements by increasing streamflows as called for by the National Oceanic and Atmospheric Administration Fisheries Biological Opinion of 2000. These study results 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.
Hydraulic and habitat simulation models contained in Physical Habitat Simulation System model were used to characterize the instream physical attributes (depth, velocity, substrate, and cover) over a range of expected summer (July through September) discharges. The final output is expressed as weighted usable area (WUA) for a representative stream segment. Continuous summer water temperature data for selected study sites also are summarized and compared with Idaho Water Quality Standards and various temperature requirements of targeted fish species.
Climatic and hydrologic conditions in the upper Salmon River Basin generally were below normal (30-year record, 1971–2000 for climatic conditions; long-term means for hydrologic conditions) during water year 2005 (WY05). Monthly snowpack levels were significantly below normal between January 1 and June 1, 2005. Average air temperature during WY05 was slightly higher than the 30-year average, whereas the average monthly air temperatures were both above and below average. Annual mean streamflows in the basin were significantly below the long-term means, as were monthly mean streamflows.
Mean air temperature at Stanley, Idaho, during WY05 was about 1.94 degrees Celsius (ºC) (35.5 degrees Fahrenheit [ºF]), slightly higher than the 30‑year (1971-2000) mean of 1.78ºC (35.2ºF). Annual mean streamflows at the long-term U.S. Geological Survey streamflow-gaging stations on Valley Creek at Stanley (13295000; 65 years of record) and on the Salmon River below Yankee Fork (13296500; 75 years of record) for WY05 were about 30 percent below the long-term means.
The lower Big Boulder Creek discharges required for maximum WUA ranged from 24 to 39 cubic feet per second (ft3/s) for adult and spawning bull trout, Chinook salmon, and steelhead trout. Discharge required for maximum WUA was 24 ft3/s for Ephemeroptim, Plecoptera, and Trichoptera (EPT) taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 18 to 27 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and 15 to 27 ft3/s greater than 10 percent of the contiguous channel width, respectively. Median discharge estimates were 32.1 ft3/s for July, 15.1 ft3/s for August, and 10.7 ft3/s for September. The mean annual discharge estimate was 15.2 ft3/ s.
Analysis of the stream temperature records for the two sites on Big Boulder Creek indicated a slight warming trend downstream. Individual metric calculation results showed the maximum daily-maximum temperature (MDMT) was well below the MDMT threshold of 21.0ºC that would block adult Chinook salmon from migrating to their spawning grounds. The MDMT at the two sites on Big Boulder Creek also was below the 18.0ºC threshold that may block bull trout migration. Temperature regimes at both sites were below Idaho Department of Environmental Quality’s (IDEQ) criteria of 19.0ºC maximum daily-average temperature (MDAT) and 22.0ºC MDMT.
Upper Challis Creek discharges required for maximum WUA ranged from 22 to 37 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout. Discharge required for maximum WUA was 16 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 16 to 22 ft3/s for the depth criterion of 0.6 feet (ft) greater than 25 percent of the total channel width and 10 to 19 ft3/s greater than 10 percent of the contiguous channel width, respectively. Median discharge (Q.50) estimates were 17.3 ft3/s for July, 8.7 ft3/s for August, and 6.9 ft3/s for September. The mean annual discharge estimate was 17.4 ft3/s.
Lower Bear Creek discharges required for maximum WUA ranged from 8 to 26 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout. Discharge required for maximum WUA was 11 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 5 to 14 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and 4 to 14 ft3/s greater than 10 percent of the contiguous channel width, respectively. Median discharge (Q.50) estimates were 10.1 ft3/s for July, 5.1 ft3/s for August, and 3.8 ft3/s for September. The mean annual discharge estimate was 8.9 ft3/s.
Upper middle Challis Creek discharges required for maximum WUA ranged from 19 to 67 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout. Discharge required for maximum WUA was 27 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from less than 11 to 23 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and less than 11 to 11 ft3/s greater than 10 percent of the contiguous channel width, respectively. Median discharge (Q.50) estimates were 47.8 ft3/s for July, 24.0 ft3/s for August, and 19.9 ft3/s for September. The mean annual discharge estimate was 46.6 ft3/s.
Lower Mill Creek discharges required for maximum WUA ranged from 9 to 18 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout. Discharge required for maximum WUA was 9 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 6 to 9 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and 3 to 9 ft3/s greater than 10 percent of the contiguous channel width, respectively. Median discharge (Q.50) estimates were 11.7 ft3/s for July, 6.0 ft3/s for August, and 4.9 ft3/s for September. The mean annual discharge estimate was 15.4 ft3/s.
Lower middle Challis Creek discharges required for maximum WUA ranged from 26 to 50 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout. Discharge required for maximum WUA was 22 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from less than 6 to 18 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and less than 6 to 14 ft3/s greater than 10 percent of the contiguous channel width, respectively. Median discharge (Q.50) estimates were 59.6 ft3/s for July, 29.9 ft3/s for August, and 25.5 ft3/s for September. The mean annual discharge estimate was 64.5 ft3/s.
Lower Challis Creek discharges required for maximum WUA ranged from 15 to 55 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout. Discharge required for maximum WUA was 35 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from 15 to 19 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and 7 to 11 ft3/s greater than 10 percent of the contiguous channel width, respectively. Median discharge (Q.50) estimates were 59.2 ft3/s for July, 29.8 ft3/s for August, and 26.1 ft3/s for September. The mean annual discharge estimate was 74.1 ft3/s.
Analysis of the stream temperature records for Challis Creek indicated a slight cooling trend downstream of upper Challis Creek to lower middle Challis Creek and then a pronounced warming trend downstream of lower middle Challis Creek to lower Challis Creek. This warming trend appears to strengthen over time and most likely is due to increasing air temperatures and the diversion of streamflow for irrigation over the course of the summer. The MDAT at upper Challis, upper middle Challis, and lower middle Challis Creek sites was below, although the MDAT at lower Challis Creek was above, the 17.8ºC MDAT upper temperature threshold that can decrease the survival rate of summer Chinook salmon juveniles in natal streams. The MDMT at all sites was very near or above the MDMT threshold of 21.0ºC that can create a thermal barrier that would block adult Chinook salmon from migrating to their spawning grounds. The MDMT at all sites exceeded the 18.0ºC threshold that may block bull trout migration. The temperature regime at all sites except lower Challis Creek was below the 19.0ºC MDAT and below the 22.0ºC MDMT IDEQ criteria, for protection of coldwater biota.
Individual metric calculation results showed that the MDAT was 11.4ºC at lower Bear Creek, well below the 17.8ºC MDAT upper temperature threshold that can decrease the survival rate of summer Chinook salmon juveniles in natal streams. The MDMT was 14.4ºC at lower Bear Creek, well below the 18.0ºC threshold that may limit bull trout habitat and block passage as a result of high water temperatures. The MDMT also was below the 21.0ºC threshold that can create a thermal barrier that can possibly block adult Chinook salmon from migrating to their spawning grounds. The temperature regime at lower Bear Creek also was below the 19.0ºC MDAT and 22.0ºC MDMT IDEQ criteria for the protection of coldwater biota.
Individual metric calculation results showed that the MDAT was 18.1ºC at lower Mill Creek, slightly above the 17.8ºC MDAT upper temperature threshold that can decrease the survival rate of summer Chinook salmon juveniles in natal streams. The MDMT was 22.0ºC at lower Mill Creek, above the 18.0ºC threshold that may limit bull trout habitat and block passage as a result of high water temperatures. The MDMT at lower Mill Creek also was above the 21.0ºC threshold that can create a thermal barrier that can possibly block adult Chinook salmon from migrating to their spawning grounds. Comparison of the temperature regime at lower Mill Creek with the IDEQ criteria of 19.0ºC MDAT and 22.0ºC MDMT for the protection of coldwater biota indicates that the MDAT was below the 19.0ºC criterion while the MDMT was at the 22.0ºC MDMT criterion.
The lower Morgan Creek discharges required for maximum WUA ranged from 15 to 42 ft3/s for adult and spawning bull trout, Chinook salmon, and steelhead trout. Discharge required for maximum WUA was 30 ft3/s for EPT taxa in riffle habitat. Discharges required for adult passage over three shallow riffle habitat transects ranged from less than 11 to 15 ft3/s for the depth criterion of 0.6 ft greater than 25 percent of the total channel width and less than 11 ft3/s greater than 10 percent of the contiguous channel width, respectively. Median discharge (Q.50) estimates were 31.2 ft3/s for July, 16.4 ft3/s for August, and 14.9 ft3/s for September. The mean annual discharge estimate was 55.5 ft3/s.
Analysis of the stream temperature records for Morgan Creek indicated a pronounced warming trend downstream of Morgan Creek above Alder Creek to lower Morgan Creek. This warming trend appears to strengthen over time and most likely is due to increasing air temperatures and the diversion of streamflow for irrigation over the course of the summer. Individual metric calculation results showed the MDAT was 14.8ºC at Morgan Creek above Alder Creek, 18.6ºC at Morgan Creek above West Fork Morgan Creek, and 19.0ºC at lower Morgan Creek. The MDAT at Morgan Creek above Alder Creek was below, while the MDAT at Morgan Creek above West Fork Morgan Creek and lower Morgan Creek was above, the 17.8ºC MDAT upper temperature threshold that can decrease the survival rate of summer Chinook salmon juveniles in natal streams. The MDMT at Morgan Creek above Alder Creek was below while the MDMT at Morgan Creek above West Fork Morgan Creek and lower Morgan Creek was above the MDMT threshold of 21.0ºC that can create a thermal barrier that would block adult Chinook salmon from migrating to their spawning grounds. The MDMT at all sites exceeded the 18.0ºC threshold that may block bull trout migration.
The temperature regime at Morgan Creek above Alder Creek was below the 19.0ºC MDAT and below the 22.0ºC MDMT IDEQ criteria, for protection of coldwater biota. The temperature regime at Morgan Creek above West Fork Morgan Creek was below the 19.0ºC MDAT but above the 22.0ºC MDMT criteria. The temperature regime at lower Morgan Creek was above the 19.0ºC MDAT and above the 22.0ºC MDMT criteria.
U.S.
Department of the Interior | U.S. Geological
Survey
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