Volume 072 Article 01 FEDERAL AID IN FISH RESTORATION SURVEY OF POTENTIAL AND AVAILABLE SALMONID HABITAT IN THE BOISE RIVER Job Completion Report Project F-71-R-12, Subproject III, Job No. 3 Prepared for: IDAHO DEPARTMENT OF FISH AND GAME By G. Asbridge and T.C. Bjornn Idaho Cooperative Fish and Wildlife Research Unit University of Idaho Moscow, Idaho 83843 June 1988 TABLE OF CONTENTS ABSTRACT ......................................................... 1 OBJECTIVES ....................................................... 2 RECOMMENDATIONS .................................................. 2 INTRODUCTION ..................................................... 3 STUDY AREA ....................................................... 5 TECHNIQUES ...................................................... 11 Habitat classification survey ............................... 11 Physical habitat measurements ............................... 12 Water temperature ............................................ 17 Estimates of fish abundance ................................. 17 Identification of limiting factors .......................... 19 Identification of improvement measures ...................... 19 FINDINGS ........................................................ 20 Habitat classification survey ............................... 20 Physical habitat measurements ............................... 28 Width .................................................. 28 Depth ................................................... 30 Water velocity .......................................... 30 Substrate composition .................................. 44 Cover .................................................. 52 Water temperature ........................................... 56 Fish abundance .............................................. 56 DISCUSSION ...................................................... 64 LITERATURE CITED ................................................ 68 i LIST OF TABLES 1. Visual substrate codes used on the Boise River and Loggers Creek during the summer of 1986 and 1987. The dominant substrate size class was recorded as X, and Y was the percent embeddedness of X ................................................ 12 2. Visual bank and instream cover codes used for seven sites on Loggers Creek during the summer of 1986. Cover objects were anything providing a significant velocity shelter or visual barrier for juvenile fish. .14 3. Visual bank and instream cover codes used on the Boise River and three sites on Loggers Creek during the summers of 1986 and 1987. Variables were recorded as X/Y/Z where X was cover status, Y was the dominant cover type, and Z was the percent of Y in each cell. Cover objects were anything providing a significant velocity shelter or visual barrier for juvenile fish. Aquatic vegetation was counted only if it provided cover. Canopy had to be greater than 3 m above the water surface and breaking the planes of the cell . .14 4. Number of pool, run and riffle habitat units measured for detailed analysis and total number of transects established for those units in the five Boise River sections and Loggers Creek during summer, 1986 and 1987, and during October 1987 for Boise River sections 1 and 2 . 16 5. Number of classifications made during habitat classification surveys on the Boise River and Loggers Creek in 1986 and 1987 . 23 6. Estimated surface areas (m2) and associated standard deviations (in parentheses) of pool, run and riffle habitat in the Boise River and Loggers Creek during the summer flow period ................................................ 24 7. Mean habitat type surface areas (m2) and associated standard deviations (in parentheses) in the Boise River and Loggers Creek during the summer flow period . .25 8. Mean habitat unit widths (m), lengths (m), standard errors (in parentheses), the number of transects used for width calculations and the number of habitat units for length calculations for each Boise River study section and the study area during 1986 and 1987 summer flow periods. Boundary transects were included for width mean and range calculations ................................................. 26 ii 9. Estimated numbers and associated standard deviations (in parentheses) of pool, run and riffle habitat units in the Boise River from Barber Dam to Star and Loggers Creek during summer, and for Boise River sections 1 and 2 during low flow periods. Only one pool was surveyed in section 1 during the low flow period, therefore a pool standard deviation was not calculated. No riffles were surveyed in section 2 during the low flow period so a number estimate was not possible . .. .27 10. Mean habitat unit widths (m), lengths (m), depths (m), velocities (m/s), ranges, and number of measurements for Loggers Creek. Width measurements equalled the number of transects per habitat type surveyed, length measurements equalled the number of habitat units surveyed (except pools where one length was not measured), depth and velocity measurements were taken at numerous points along each transect. Boundary transects were included for width calculations, but not for depth and velocity calculations. Habitat units were surveyed during the summer of 1986 . .. .28 11. Mean widths, depths and velocities for habitat units measured during summer and October, 1987, in the Boise River. Boundary transects were included to calculate means. For each habitat unit n = 3. Vertical lines to the right of two values indicate no significant difference between the values (alpha 0.05, paired t test) . .. .42 12. Mean habitat type depths (m), velocities (m/s), ranges (in parentheses), and number of measurements for Boise River sections and study area for 1986 and 1987 summer flow periods. Boundary transects were excluded when calculating means and ranges ......................................43 13. Percent relative abundance of three water velocity classes presented graphically in Figures 12, 14, 16, and 25 for two pools and two runs in the Boise River. Water velocity was measured every 15.2 cm depth interval of each vertical during the summer of 1987 . 52 14. Number of salmonids collected by electrofishing from six sites in the Boise River on 25, 26, and 27 October, 1986 while flows were low (169 cfs at Barber Park and 145 cfs at Glenwood Bridge) . 62 15. Number of salmonids counted by snorkeling in Boise River and Loggers Creek study sites during August 1986. Mountain whitefish size classes were 0 to 100 mm (age 0), 101 to 200 mm (age 1), and > 200 mm (age 2+). Rainbow and brown trout size classes were 0 to 85 mm (age 0), 86 to 200 mm (age 1), and > 200 mm (age 2+) . 63 iii LIST OF FIGURES 1. Unregulated and regulated discharge of the Boise River at Lucky Peak Dam for water years 1986 and 1987. Unregulated discharge is calculated by the United States Army Corps of Engineers and simulates natural flow in the river without the three upstream dams . .. 4 2. Map of the Boise River from its origin at Lucky Peak Dam to Star, Idaho. The study area extended from Barber Dam to Star, a distance of 40.2 kilometers . .. 6 3. Boise River mean daily discharge from Lucky Peak Dam and at the At Boise gaging station during water years 1978 through 1982 . .. 7 4. Boise River mean daily discharge from Lucky Peak Dam and at the Glenwood Bridge gaging station for water years 1983 through 1987 . .. 8 5. Boise River mean daily discharge from Lucky Peak Dam and at the Glenwood Bridge gaging station for water years 1986 and 1987 . .. 9 6. Schematic diagram of a study site in the Boise River and Loggers Creek with three transects. Areas 1, 2 and 3 were the sums of cell areas associated with transects 1, 2 and 3, respectively . .. 13 7. Major irrigation diversions and electronic temperature recorder locations in the Boise River from Lucky Peak Dam to Star . 18 8. Relative abundance of pool, run and riffle habitat in the Boise River and Loggers Creek, including associated 95% confidence intervals. Summer habitat classification surveys were completed during June and July 1986; low flow surveys were completed in December 1986, April 1987 and October 1987 . 21 9. Relative abundance of pool, run and riffle habitat in Boise River sections during summer (top) and low flow (bottom) periods, including 95% confidence intervals. Summer habitat classification surveys were completed during June and July 1986, and low flow surveys were completed in December 1986, April 1987 and October 1987 . 22 10. Mean study section widths, depths, and habitat type velocities in each section in the Boise River from Barber Dam to Star. Measurements were taken during 1986 and 1987 summers. A horizontal line across two or more bars indicates no significant difference between those sections or habitat types ............................................................ 29 iv 11. Overhead map with depth isopleths of Pool 3, section 1 in the Boise River which was surveyed in August and October 1987. .31 12. Transect cross sections from Pool 3, section 1 in the Boise River in summer and October 1987. For summer cross sections the clear areas had velocities < 0.20 m/s, cross hatched areas had velocities from 0.20 to 0.40 m/s and black areas had velocities > 0.40 m/s. In October, velocity was taken at 0.6 total depth so only wetted perimeter, depth and mean transect water velocity (calculated with 0.6 depth velocities) can be compared between summer and October. Sample sizes (n) were the number of measurements across each transect .......................................................... 32 13. Overhead map