U.S. Department of the Interior U.S. Geological Survey Prepared in cooperation with the IDAHO DIVISION OF ENVIRONMENTAL QUALITY and LOWER BOISE RIVER WATER QUALITY PLAN, INC. Biological Assessment of the Lower Boise River, October 1995 Through January 1998, Ada and Canyon Counties, Idaho Water-Resources Investigations Report 99–4178 Biological Assessment of the Lower Boise River, October 1995 Through January 1998, Ada and Canyon Counties, Idaho By William H. Mullins Water-Resources Investigations Report 99–4178 Prepared in cooperation with the IDAHO DIVISION OF ENVIRONMENTAL QUALITY and LOWER BOISE RIVER WATER QUALITY PLAN, INC. Boise, Idaho 1999 U.S. DEPARTMENT OF THE INTERIOR BRUCE BABBITT, Secretary U.S. GEOLOGICAL SURVEY Charles G. Groat, Director Any use of firm, trade, and brand names in this report is for identification purposes only and does not constitute endorsement by the U.S. Government. Additional information can be obtained from: Copies of this report can be purchased from: District Chief U.S. Geological Survey U.S. Geological Survey Information Services 230 Collins Road Box 25286 Boise, ID 83702-4520 Federal Center http://idaho.usgs.gov Denver, CO 80225 e-mail: [email protected] CONTENTS Abstract.................................................................................................................................................................................... 1 Introduction ............................................................................................................................................................................. 1 Purpose and scope.......................................................................................................................................................... 2 Acknowledgments ......................................................................................................................................................... 2 Description of the lower Boise River Basin ............................................................................................................................ 2 Previous investigations ............................................................................................................................................................ 4 Methods of data collection and analysis.................................................................................................................................. 6 Instream and riparian habitat ......................................................................................................................................... 6 Epilithic periphyton ....................................................................................................................................................... 7 Benthic macroinvertebrates ........................................................................................................................................... 7 Fish................................................................................................................................................................................. 8 Biological assessment.............................................................................................................................................................. 9 Instream and riparian habitat ......................................................................................................................................... 9 Epilithic periphyton ....................................................................................................................................................... 11 Benthic macroinvertebrates ........................................................................................................................................... 11 Fish................................................................................................................................................................................. 26 Summary and conclusions ....................................................................................................................................................... 28 References cited....................................................................................................................................................................... 29 Appendices: A. Habitat assessment field data sheet ........................................................................................................................ 33 B. Locations of stakes for permanent transects at habitat assessment sites, Boise River, Idaho, November 1997 through January 1998 .................................................................................................................. 35 C. Detailed instream habitat variables measured in the Boise River, Idaho, November 1997 through January 1998............................................................................................................................................. 36 D. Detailed riparian habitat variables measured in the Boise River, Idaho, November 1997 through January 1998............................................................................................................................................. 37 FIGURES 1. Map showing location of lower Boise River Basin, Idaho, and six sampling sites........................................................ 3 2. Graph showing annual mean discharge and mean monthly discharge in the lower Boise River near Parma, Idaho, water years 1975–96 ................................................................................................................................................. 5 3. Graph showing pebble count data for the lower Boise River, Idaho, November 1997 through January 1998.............. 10 4. Map showing general site plan and individual transects, lower Boise River at Eckert Road (site 1), Idaho, November 1997 ......................................................................................................................................................... 12 5. Channel transects for the lower Boise River at Eckert Road (site 1), Idaho, November 1997 ...................................... 13 6. Map showing general site plan and individual transects, lower Boise River near Middleton (site 4), Idaho, November 1997 ......................................................................................................................................................... 14 7. Channel transects for the lower Boise River near Middleton (site 4), Idaho, November 1997 .....................................15 8. Map showing general site plan and individual transects, lower Boise River at mouth near Parma (site 6), Idaho, January 1998.............................................................................................................................................................. 16 9. Channel transects for the lower Boise River at mouth near Parma (site 6), Idaho, January 1998 .................................17 10. Graph showing spatial and temporal trends of chlorophyll-a and ash-free dry weight for epilithic periphyton in the lower Boise River, Idaho, October 1995, October 1996, and August 1997....................................................18 11. Graph showing benthic index of biotic integrity scores for macroinvertebrates collected in the lower Boise River, Idaho, during October 1995, 1996, and 1997............................................................................................................ 27 Contents -1iii TABLES 1. Sampling site locations, types of samples collected, and dates of collection, lower Boise River, Idaho, 1995–98..................................................................................................................................................................... 8 2. Habitat variables measured in the lower Boise River, Idaho, November 1997 through January 1998 .......................... 9 3. Habitat variables for the lower Boise River, Idaho, assessed using rapid bioassessment protocols, November 1997 through January 1998................................................................................................................................................. 11 4. Chlorophyll-a and ash-free dry weight of epilithic periphyton collected in the lower Boise River, Idaho, October 1995, October 1996, and August 1997 ........................................................................................................ 19 5. Mean density of macroinvertebrate taxa collected in the lower Boise River, Idaho, October 1995, 1996, and 1997.... 20 6. Macroinvertebrate community metrics for taxa collected in the lower Boise River, Idaho, October 1995, 1996, and 1997..................................................................................................................................................................... 23 7. Scoring criteria for macroinvertebrate community metrics used to assess biotic integrity of the lower Boise River, Idaho ..................................................................................................................................................... 23 8. Benthic index of biotic integrity scores for macroinvertebrates collected in the lower Boise River, Idaho, October 1995, 1996, and 1997................................................................................................................................... 24