Prepared in cooperation with the Bureau of Reclamation Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005 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 2006–5230 U.S. Department of the Interior U.S. Geological Survey Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005 By Terry R. Maret, Jon E. Hortness, and Douglas S. Ott Prepared in cooperation with the Bureau of Reclamation Scientific Investigations Report 2006–5230 U.S. Department of the Interior U.S. Geological Survey U.S. Department of the Interior DIRK A. KEMPTHORNE, Secretary U.S. Geological Survey Mark D. Myers, Director U.S. Geological Survey, Reston, Virginia: 2006 For product and ordering information: World Wide Web: http://www.usgs.gov/pubprod Telephone: 1-888-ASK-USGS For more information on the USGS--the Federal source for science about the Earth, its natural and living resources, natural hazards, and the environment: World Wide Web: http://www.usgs.gov Telephone: 1-888-ASK-USGS Any use of trade, product, or firm names 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., 2006, Instream flow characterization of upper Salmon River Basin streams, central Idaho, 2005: U.S. Geological Survey Scientific Investigations Report 2006-5230, 110 p. iii Contents Abstract ...........................................................................................................................................................1 Introduction.....................................................................................................................................................1 Purpose and Scope ..............................................................................................................................3 Previous Studies ...................................................................................................................................3 Description of Study Area ...................................................................................................................5 Data Collection Methods ..............................................................................................................................7 Site Selection ........................................................................................................................................7 Environmental Variables ......................................................................................................................8 Physical Habitat ...........................................................................................................................8 Stream Temperature ....................................................................................................................8 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 2005 ....................................................................................12 Climatic Conditions .............................................................................................................................12 Hydrologic Conditions ........................................................................................................................13 Results of Study Site Investigations .........................................................................................................14 Big Boulder Creek ...............................................................................................................................14 Hydrology ....................................................................................................................................14 Habitat Modeling and Passage Criteria .................................................................................14 Stream Temperature ..................................................................................................................18 Challis Creek and Major Tributaries ................................................................................................19 Hydrology ....................................................................................................................................21 Habitat Modeling and Passage Criteria .................................................................................21 Stream Temperature ..................................................................................................................24 Morgan Creek ......................................................................................................................................28 Hydrology ....................................................................................................................................28 Habitat Modeling and Passage Criteria .................................................................................28 Stream Temperature ..................................................................................................................28 Summary........................................................................................................................................................33 Acknowledgments .......................................................................................................................................35 References Cited..........................................................................................................................................35 Appendixes A-H. Plan views, weighted useable areas, and passage criteria assessments for bull trout, Chinook salmon, steelhead trout, and invertebrates for study sites in the upper Salmon River Basin, Idaho, 2005 .................................................39 iv Figures Figure 1. Map showing location of selected streamflow-gaging stations in the upper Salmon River Basin, Idaho ………………………………………………………… 6 Figure 2. Diagram showing hierarchical habitat classification used in this study. ………… 7 Figure 3. Graph showing relation between mean daily air temperatures measured at Stanley Ranger Station, June through September 2005, and long-term values (1971 through 2000), upper Salmon River Basin, Idaho …………………………… 13 Figure 4. Map showing location of study sites on lower Big Boulder Creek, diversions, streamflow-gaging stations, temperature monitoring locations, and Physical Habitat Simulation (PHABSIM) study site, upper Salmon River Basin, Idaho, 2005 ………………………………………………………………………… 16 Figure 5. Graph showing daily mean discharge at Big Boulder Creek near Clayton (13297500), upper Salmon River Basin, Idaho, April 1 through September 30, 2005 ……………………………………………………………… 17 Figure 6. Graph showing daily mean discharge for water year 2005 and 80-, 50-, and 20-percent exceedance statistics for the period of record (1926–29, 2005) at Big Boulder Creek near Clayton (13297500), upper Salmon River Basin, Idaho, July 1 through September 30 ……………………………………………………… 17 Figure 7. Graph showing maximum daily water temperature at Big Boulder Creek, upper Salmon River Basin, Idaho, June 12 through September 12, 2005 ………………… 19 Figure 8. Map showing location of study sites on Challis, Bear, and Mill Creeks, diversions, streamflow-gaging stations, temperature monitoring locations, and Physical Habitat Simulation (PHABSIM) study sites, upper Salmon River Basin, Idaho, 2005 ………………………………………………………………………… 20 Figure 9. Graph showing maximum daily water temperature at Challis Creek, upper Salmon River Basin, Idaho, June 12 through September 12, 2005 ………………… 25 Figure 10. Graph showing maximum daily water temperature at Bear Creek (BE1), upper Salmon River Basin, Idaho, June 12 through September 12, 2005 ………………… 26 Figure 11. Graph showing maximum daily water temperature at Mill Creek (ML1), upper Salmon River Basin, Idaho, June 12 through September 12, 2005 ………………… 27 Figure 12. Map showing location of study sites on Morgan Creek, diversions, streamflow- gaging stations, temperature monitoring locations, and Physical Habitat