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Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2004

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Prepared in cooperation with the Bureau of Reclamation Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2004 Ellis River Challis Fork Salmon Yankee Squaw T h o m Valley p s o n Creek Creek Creek Creek Elk Salmon River Stanley Iron Creek Salmon River Redfish Lake Obsidian July Salmon of Creek Fourth Champion Creek River Alturas Fork Lake Pole Creek Creek East Creek Beaver Smiley Scientific Investigations Report 2005–5212 U.S. Department of the Interior U.S. Geological Survey Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2004 By Terry R. Maret, Jon E. Hortness, and Douglas S. Ott Prepared in cooperation with the Bureau of Reclamation Scientific Investigations Report 2005-5212 U.S. Department of the Interior U.S. Geological Survey U.S. Department of the Interior Gale A. Norton, Secretary U.S. Geological Survey P. Patrick Leahy, Acting Director U.S. Geological Survey, Reston, Virginia: 2005 For sale by U.S. Geological Survey, Information Services Box 25286, Denver Federal Center Denver, CO 80225 For more information about the USGS and its products: Telephone: 1-888-ASK-USGS World Wide Web: http://www.usgs.gov/ Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this report is in the public domain, permission must be secured from the individual copyright owners to reproduce any copyrighted materials contained within this report. Suggested citation: Maret, T.R., Hortness, J.E., and Ott, D.S., 2005, Instream flow characterization of upper Salmon River Basin streams, Central Idaho, 2004: U.S. Geological Survey Scientific Investigations Report 2005-5212, 124 p. iii Contents Abstract ……………………………………………………………………………………… 1 Introduction …………………………………………………………………………………… 1 Purpose and Scope ……………………………………………………………………… 3 Previous Studies ………………………………………………………………………… 3 Description of Study Area ……………………………………………………………… 5 Acknowledgments ……………………………………………………………………… 7 Data Collection Methods ……………………………………………………………………… 7 Site Selection …………………………………………………………………………… 7 Environmental Variables ………………………………………………………………… 8 Physical Habitat …………………………………………………………………… 8 Stream Temperature ……………………………………………………………… 9 Analytical Methods for Instream Flow Characterization ……………………………………… 9 Physical Habitat Simulation Model ……………………………………………………… 9 Hydraulic Modeling and Calibration………………………………………………… 9 Habitat Modeling …………………………………………………………………… 9 Selection of Target Species and Habitat Suitability Criteria ………………… 9 Passage Criteria ……………………………………………………………… 10 Stream Temperature …………………………………………………………………… 11 Guidelines for Using Study Results ……………………………………………………… 11 Climatic and Hydrologic Conditions During 2004 ……………………………………………… 13 Climatic Conditions ……………………………………………………………………… 13 Hydrologic Conditions …………………………………………………………………… 14 Results of Study Site Investigations ………………………………………………………… 14 Salmon River …………………………………………………………………………… 14 Hydrology …………………………………………………………………………… 14 Habitat Modeling and Passage Criteria …………………………………………… 20 Stream Temperature ……………………………………………………………… 20 Beaver Creek …………………………………………………………………………… 22 Hydrology …………………………………………………………………………… 23 Habitat Modeling and Passage Criteria …………………………………………… 25 Stream Temperature ……………………………………………………………… 25 Pole Creek ……………………………………………………………………………… 26 Hydrology …………………………………………………………………………… 26 Habitat Modeling and Passage Criteria …………………………………………… 28 Stream Temperature ……………………………………………………………… 29 iv Contents—Continued Champion Creek ………………………………………………………………………… 30 Hydrology …………………………………………………………………………… 30 Habitat Modeling and Passage Criteria …………………………………………… 32 Stream Temperature ……………………………………………………………… 32 Fourth of July Creek ……………………………………………………………………… 34 Stream Temperature ……………………………………………………………… 34 Description of Stream Temperature Model ………………………………………… 36 Model Setup ………………………………………………………………… 36 Model Structure ……………………………………………………………… 36 Model Calibration …………………………………………………………… 37 Evaluating the Effects of Diversions on Stream Temperature ………………… 37 Iron Creek ……………………………………………………………………………… 37 Hydrology …………………………………………………………………………… 40 Habitat Modeling and Passage Criteria …………………………………………… 42 Stream Temperature ……………………………………………………………… 42 Thompson Creek ………………………………………………………………………… 44 Hydrology …………………………………………………………………………… 44 Habitat Modeling and Passage Criteria …………………………………………… 44 Stream Temperature ……………………………………………………………… 44 Squaw Creek …………………………………………………………………………… 48 Hydrology …………………………………………………………………………… 48 Habitat Modeling and Passage Criteria …………………………………………… 51 Stream Temperature ……………………………………………………………… 51 Summary ……………………………………………………………………………………… 53 References Cited ……………………………………………………………………………… 55 Appendixes A-G. Plan views, weighted useable areas, and passage criteria assessments for bull trout, Chinook salmon, and steelhead trout for study sites in the upper Salmon River Basin, Idaho, 2004 ……………………………………………… 59 v Figures Figure 1. Map showing location of upper Salmon River Basin, Idaho ……………………… 6 Figure 2. Diagram showing hierarchical habitat classification used in this study ………… 8 Figure 3. Graph showing relation between mean daily air temperatures measured at Stanley Ranger Station for June through September 2004 and long-term values (1971 through 2000), upper Salmon River, Idaho …………………………… 13 Figure 4. Map showing location of study sites on Beaver and Pole Creeks and Salmon River, diversions, streamflow-gaging stations, irrigation pumps, and temperature monitoring locations, upper Salmon River Basin, Idaho, 2003–04 …… 17 Figure 5. Graph showing daily mean discharge at Salmon River at Pole Creek Road above diversions, near Obsidian (13292280), upper Salmon River Basin, Idaho, April 1 through September 30, 2004 ……………………………………… 18 Figure 6. Graph showing daily mean discharge for water year 2004, estimated long-term daily mean discharge, and estimated 80-, 50-, and 20-percent exceedance statistics at Salmon River at Pole Creek Road above diversions, near Obsidian (13292280), upper Salmon River Basin, Idaho, July 1 through September 30 ……………………………………………………………………… 19 Figure 7. Graph showing maximum daily water temperature at Salmon River, upper Salmon River Basin, Idaho, June 20 through September 28, 2003 ………………… 21 Figure 8. Graph showing maximum daily water temperature, at Salmon River, upper Salmon River Basin, Idaho, June 9 through September 30, 2004 ………………… 22 Figure 9. Graph showing daily mean discharge at Beaver Creek at Highway 75 Bridge, near Stanley (BCHWY75), upper Salmon River Basin, Idaho, May 10 through September 30, 2004 ……………………………………………………… 23 Figure 10. Graph showing daily mean discharge for water year 2004, estimated long-term daily mean discharge, and estimated 80-, 50-, and 20-percent exceedance statistics at Beaver Creek at Highway 75 bridge, near Stanley, upper Salmon River Basin, Idaho, July 1 through September 30 ………………… 24 Figure 11. Graph showing maximum daily water temperature at Beaver Creek, upper Salmon River Basin, Idaho, June 9 through September 30, 2004 ………………… 26 Figure 12. Graph showing daily mean discharge at Pole Creek below Pole Creek Ranger Station, near Obsidian (13292380), upper Salmon River Basin, Idaho, April 1 through September 30, 2004 ……………………………………………… 27 Figure 13. Graph showing daily mean discharge for water year 2004, estimated long-term daily mean discharge and estimated 80-, 50-, and 20-percent exceedance statistics at Pole Creek below Pole Creek Ranger Station, near Obsidian (13292380), upper Salmon River Basin, Idaho, July 1 through September 30 ……………………………………………………………………… 27 Figure 14. Graph showing maximum daily water temperature at Pole Creek, upper Salmon River Basin, Idaho, June 9 through September 30, 2004 ………………… 29 Figure 15. Maps showing location of study sites on Champion and Fourth of July Creeks and Salmon River, diversions, streamflow-gaging stations, and temperature monitoring locations, upper Salmon River Basin, Idaho, 2003-04 …… 31 Figure 16. Graph showing maximum daily water temperature at Champion Creek, upper Salmon River Basin, Idaho, June 9 through September 30, 2004 …………… 33 Figure 17. Graph showing maximum daily water temperature at Fourth of July Creek, upper Salmon River Basin, Idaho, June 9 through September 30, 2004 …………… 34 vi Figures—Continued Figure 18. Graphs showing daily mean discharges at Fourth of July Creek above diversions, near Obsidian (13293350), and Fourth of July Creek at Highway 75 bridge, near Obsidian (Idaho Power Company), upper Salmon River Basin, Idaho, May 10 through September 30, 2004 ……………………………… 35 Figure 19. Graphs showing comparison of measured stream temperatures with predicted stream temperatures at Fourth of July Creek, upper Salmon River Basin, Idaho, July 31, 2003 ………………………………………………………… 38 Figure 20. Maps showing location of study sites on Iron Creek, diversions, and streamflow-gaging stations, upper Salmon River Basin, Idaho, 2004 …………… 39 Figure 21. Graph showing daily mean discharge at Iron Creek above diversions, near Stanley (13294880), upper Salmon River Basin, Idaho, April 1 through September 30, 2004 ……………………………………………………………… 40 Figure 22. Graph showing daily mean discharge for water year 2004, estimated long-term daily mean discharge, and estimated 80-, 50-, and 20-percent exceedance statistics at Iron Creek above diversions, near Stanley (13294880), upper Salmon River Basin, Idaho, July 1 through September 30 ……… 41 Figure 23. Graph showing maximum
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