State of California The Resources Agency DEPARTMENT OF FISH AND GAME

State of California The Resources Agency DEPARTMENT OF FISH AND GAME FINAL REPORT SHASTA AND SCOTT RIVER JUVENILE SALMONID OUTMIGRATION MONITORING PROJECT Prepared for the Pacific States Marine Fisheries Commission Contract No. 09-62 Prepared by Kirstin Underwood, Heather D. Langendorf, Chris Diviney, Amy Debrick, Seth Daniels, Whitney B. Crombie, and William R. Chesney California Department of Fish and Game Anadromous Fisheries Resource Assessment and Monitoring Program November 2010

Table of Contents List of Figures...iii List of Tables...v List of Appendices...v Abstract...1 Background...1 Shasta River Rotary Screw Trap Summary Methods...1 Age Determination...2 Trap Efficiency Determinations and Production Estimates...2 Water Temperature and Flow Monitoring...3 Results...3 Chinook...3 Coho...3 Steelhead...4 Temperature monitoring... 5 Discussion...17 Multi-Year Estimates...17 Chinook......17 Steelhead...19 Coho......20 Scott River Rotary Screw Trap Summary Methods...22 Age Determination......22 Trap Efficiency Determinations and Production Estimates... 22 Water Temperature and Flow Monitoring...23 Results...23 Chinook...24 Coho...25 Steelhead...25 Discussion...35 Acknowledgements... 40 Literature Cited...41 ii

List of Figures Shasta River Figures Figure 1. Shasta River 0+ Chinook estimates, 2009...5 Figure 2. Shasta River 0+ Chinook estimates, as percentage of total estimate, 2009...6 Figure 3. Shasta River 0+ and 1+ Chinook weekly mean fork lengths, 2009...6 Figure 4. Shasta River 0+ coho estimates, 2009...7 Figure 5. Shasta River 0+ coho estimates, as percentage of total estimate, 2009...7 Figure 6. Shasta River 1+ coho estimates, 2009...8 Figure 7. Shasta River 1+ coho estimates, as percentage of total estimate, 2009...8 Figure 8. Shasta River 0+, 1+, and 2+ coho weekly mean fork lengths...9 Figure 9. Shasta River 0+ steelhead estimates, 2009...9 Figure 10. Shasta River 0+ steelhead estimates, as percentage of total estimate, 2009...10 Figure 11. Shasta River 1+ steelhead estimates, 2009...10 Figure 12. Shasta River 1+ steelhead estimates, as percentage of total estimate, 2009...11 Figure 13. Shasta River 0+ and 1+ steelhead weekly mean fork lengths, 2009...11 Figure 14. Shasta River 2+ steelhead estimates, 2009...12 Figure 15. Shasta River 2+ steelhead estimates, as percentage of total estimate, 2009...12 Figure 16. Shasta River 3+ steelhead estimates, 2009...13 Figure 17. Shasta River 3+ steelhead estimates, as percentage of total estimate, 2009...13 Figure 18. Shasta River 2+ and 3+ steelhead weekly mean fork lengths, 2009...14 Figure 19. Correlations between 0+ coho and 0+ steelhead trap efficiencies...14 iii

Figure 20. Correlations between 1+ coho and 2+ steelhead trap efficiencies...15 Figure 21. Shasta River 2009 flow by Julian Week...15 Figure 22. Shasta River 2009 water temperature by Julian Week....16 Figure 23. Shasta River 2009 mean, maximum, and minimum water temperatures...16 Figure 24. Shasta River 2000-2009 0+ Chinook population estimates...18 Figure 25. Shasta River 2+ 2004-2009 steelhead population estimates...20 Figure 26. Shasta River 1+ 2003-2009 coho population estimates...21 Scott River Figures Figure 27. Scott River 0+ Chinook estimates, 2009...26 Figure 28. Scott River 0+ Chinook estimates, as percentage of total estimate, 2009...27 Figure 29. Scott River 0+ and 1+ Chinook weekly mean fork lengths, 2009...27 Figure 30. Scott River 0+ coho estimates, 2009...28 Figure 31. Scott River 0+ coho estimates, as percentage of total estimate, 2009...28 Figure 32. Scott River 1+ coho estimates, 2009...29 Figure 33. Scott River 1+ coho estimates, as percentage of total estimate, 2009...29 Figure 34. Scott River 0+ and 1+ coho weekly mean fork lengths, 2009...30 Figure 35. Scott River 1+ steelhead estimates, 2009...30 Figure 36. Scott River 1+ steelhead estimates, as percentage of total estimate, 2009...31 Figure 37. Scott River 0+ and 1+ steelhead weekly mean fork lengths, 2009...31 Figure 38. Scott River 2+ steelhead estimates, 2009...32 Figure 39. Scott River 2+ steelhead estimates, as percentage of total estimate, 2009...33 Figure 40. Scott River 2+ and 3+ steelhead weekly mean fork lengths, 2009...34 Figure 41. Scott River 2009 flow by Julian Week...34 iv

Figure 42. Scott River 2009 water temperatures by Julian week...35 Figure 43. Scott River 2009 mean, maximum and minimum water temperatures...35 Figure 44. Scott River 2009 days trapped per week...36 Figure 45. Scott River 2001-2009 0+ Chinook population estimates...37 Figure 46. Scott River 2+ 2004-2009 steelhead population estimates...39 Figure 47. Scott River 1+ 2003-2009 coho population estimates...41 List of Tables Table 1. Shasta River weekly production estimates for 0+ Chinook salmon, 2000-2009.17 Table 2. Shasta River weekly production estimates for 2+ steelhead, 2004-2009...19 Table 3. Coho 1+ produced per returning adult....20 Table 4. Coho 1+ smolt to adult survival...21 Table 5. Shasta River weekly production estimates for 1+ coho salmon, 2003-2009...22 Table 6. Scott River weekly production estimates for 0+ Chinook salmon, 2001-2009...37 Table 7. Scott River weekly production estimates for 2+ steelhead, 2004-2009...38 Table 8. Scott River weekly production estimates for 1+ coho salmon, 2003-2009...40 Table 9. Yearly mark-recapture totals and corresponding estimates for 1+ coho...41 v

List of Appendices Appendix 1. Catch table with weekly data for Chinook 0+, Shasta River 2009...30 Appendix 2. Catch table with weekly data for Chinook 1+, Shasta River 2009...31 Appendix 3. Catch table with weekly data for coho 0+, Shasta River 2009...32 Appendix 4. Catch table with weekly data for coho 1+, Shasta River 2009...33 Appendix 5. Catch table with weekly data for coho 2+, Shasta River 2009...34 Appendix 6. Catch table with weekly data for steelhead 0+, Shasta River 2009...35 Appendix 7. Catch table with weekly data for steelhead 1+, Shasta River 2009...36 Appendix 8. Catch table with weekly data for steelhead 2+, Shasta River 2009...37 Appendix 9. Catch table with weekly data for steelhead 3+, Shasta River 2009...38 Appendix 10. Catch table with weekly data for Chinook 0+, Scott River 2009...39 Appendix 11. Catch table with weekly data for Chinook 1+, Scott River 2009...40 Appendix 12. Catch table with weekly data for coho 0+, Scott River 2009...41 Appendix 13. Catch table with weekly data for coho 1+, Scott River 2009...42 Appendix 14. Catch table with weekly data for steelhead 0+, Scott River 2009...43 Appendix 15. Catch table with weekly data for steelhead 1+, Scott River 2009...43 Appendix 16. Catch table with weekly data for steelhead 2+, Scott River 2009...44 Appendix 17. Catch table with weekly data for steelhead 3+, Scott River 2009...44 Appendix 18. Weekly fork length data for Chinook 0+, Shasta River 2009...45 Appendix 19. Weekly fork length data for Chinook 1+, Shasta River 2009...45 Appendix 20. Weekly fork length data for coho 0+, Shasta River 2009...46 Appendix 21. Weekly fork length data for coho 1+, Shasta River 2009...46 vi

Appendix 22. Weekly fork length data for coho 2+, Shasta River 2009...47 Appendix 23. Weekly fork length data for steelhead 0+, Shasta River 2009...47 Appendix 24. Weekly fork length data for steelhead 1+, Shasta River 2009...48 Appendix 25. Weekly fork length data for steelhead 2+, Shasta River 2009...48 Appendix 26. Weekly fork length data for steelhead 3+, Shasta River 2009...49 Appendix 27. Weekly fork length data for Chinook 0+, Scott River 2009...49 Appendix 28. Weekly fork length data for Chinook 1+, Scott River 2009...50 Appendix 29. Weekly fork length data for coho 0+, Scott River 2009...50 Appendix 30. Weekly fork length data for coho 1+, Scott River 2009...51 Appendix 31. Weekly fork length data for steelhead 0+, Scott River 2009...52 Appendix 32. Weekly fork length data for steelhead 1+, Scott River 2009...56 Appendix 33. Weekly fork length data for steelhead 2+, Scott River 2009...57 Appendix 34. Weekly fork length data for steelhead 3+, Scott River 2009...58 Appendix 35. Weekly temperature statistics, Shasta River 2009...49 Appendix 36. Weekly temperature statistics, Scott River 2009...58 Appendix 37. Age length cut-off for Shasta River juvenile salmonids...59 Appendix 38. Age length cut-off for Scott River juvenile salmonids...60 Appendix 39. Additional fish species collected in the Shasta and Scott River rotary traps, 2009...53 Appendix 40. List of Julian weeks and calendar equivalents...54 vii

Abstract 2009 was the tenth consecutive year of rotary trapping on the Shasta and Scott rivers. The goals of the project were to determine emigration abundance and timing of all age classes of juvenile salmonids leaving the Shasta and Scott rivers between early February and early July 2009, and to investigate the relationships between in-stream conditions and emigration patterns of juvenile salmonids. Trap efficiencies were determined for all age classes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss) in the catch, and weekly production estimates were calculated for each age class. The weekly mean fork length for all age classes of salmonids in the catch was determined from a measured sub-sample. Due to low numbers of coho expected in 2009, the correlation between 0+ steelhead trap efficiencies and 0+ coho efficiencies observed in previous years was used to produce estimates of trap efficiencies in 2009. The same method was followed with 2+ steelhead efficiencies to provide 1+ coho efficiencies. Background 2009 was the tenth consecutive year of rotary trapping on the Shasta and Scott rivers. The goals of the project were: To determine emigration abundance and timing of all age classes of juvenile salmonids exiting the Shasta and Scott rivers between early February and early July 2009. To investigate the relationships between in-stream conditions and emigration patterns of juvenile salmonids. The specific objectives were: To estimate the weekly mean fork length at age of salmonids in the catch from a measured sub-sample. To estimate weekly rotary trap efficiencies for all age classes of Chinook, coho and steelhead in the catch and produce weekly production estimates for each age class. To monitor stream flow and temperature at the traps. Shasta River Rotary Screw Trap Summary Methods The Shasta River was sampled with a modified five foot rotary screw trap manufactured by EG Solutions, Corvallis, Oregon. The trap was operated six days per week: Sunday afternoon through Saturday morning, directly downstream of the Shasta River Fish Counting Facility at 041º 49' 46.38" N, 122º 35' 35.38" W. The catch in the trap was processed daily at approximately 0800 hrs. The live car was checked and algae build-up was removed at approximately 1700 hours and at 2200 hours daily as needed. The velocity of the water entering the cone was measured at the beginning and end of each set with a flow meter manufactured by General Oceanics, model 2030R. Total volume sampled was calculated for each set. All vertebrates collected in the trap were identified and counted. Salmonids collected in the trap were classified by species, age and life stage. Scale samples and fork length data were collected from a random sample of salmonids in the catch. 1

Age Determination The same age length cutoffs for salmonids developed in 2007 were used in 2009. These cutoffs were determined from fork length frequency distributions and by estimating the age of scales in the 2001-2007 collection. Individual scale samples were visually examined and categorized into brood years using scale age-estimation methods (Van Oosten 1957, Chilton and Beamish 1982, Casselman 1983). Fork length intervals for each age class were determined for appropriate time periods and updated throughout the season. The intervals are not absolute and as a result of variable growth, some individuals may be larger or smaller than the cutoff fork length. The fork length cutoffs and the number of scales examined to determine the cutoffs are shown in Appendices 37. Trap Efficiency Determinations and Production Estimates When sufficient fish were in the catch, multiple trap efficiency trials were conducted to determine the mean weekly trap efficiency for 0+ Chinook (Oncorhynchus tshawytscha), 1+ coho (Oncorhynchus kisutch), and 0+, 1+, 2+, and 3+ steelhead (Oncorhynchus mykiss). For each trial, a known number of marked fish from each age class were taken three quarters of a mile upstream from the trap and released. 0+ salmonids were dyed by placing them in a solution of 0.6 grams of Bismarck brown mixed with 19 liters of water for 40 to 50 minutes. The older age fish were marked with a caudal fin margin clip. Three different caudal fin margin clips were used in a weekly rotation allowing us to determine if marked fish were being recaptured outside of the week in which they were marked. Fish marked in the morning processing were held in live cars until the afternoon in order to assess their condition prior to release. For each species and age class, the number of fish recaptured during the week divided by the total number marked equals the estimated trap efficiency for the week. An estimate of the total number of outmigrants per week was determined using a stratified mark and recapture technique (Carlson 1998). Zero was used for the lower confidence limit if the calculated lower confidence limit for the estimate was negative. In weeks when marked fish were released but none were recaptured, the seasonal trap efficiency was used to expand the number of fish trapped to develop an estimate of the total migrants for the week (ODFW Salmonid Lifecycle Monitoring Project). Estimating trap efficiencies for coho In 2009, during weeks of low abundance we chose to minimize our handling of coho and did not attempt mark-recapture trials. Known trap efficiencies between 0+ coho and 0+ steelhead from previous years were correlated to provide a weekly population estimate for 0+ coho. A correlation between 2+ steelhead and 1+ coho trap efficiencies from previous years was used to provide a weekly population estimate for 1+ coho. The correlation between 0+ steelhead and 0+ coho trap efficiencies in 2005, 2006 and 2008 was expressed by the equation y = 0.8224x + 0.0039 (Figure 19). The weekly efficiencies for 0+ steelhead from 2009 were equal to X and we solved for Y to estimate the trap efficiency for 0+ coho. When no 0+ steelhead were marked during the week, the seasonal trap efficiency of 15.83% was used to estimate the number of coho fry produced in 2009. When marked 0+ steelhead were released but none were recaptured during the week, the seasonal trap efficiency was correlated using the above equation to provide an efficiency for 0+ coho. 2

The correlation between the trap efficiency for 2+ steelhead smolts and 1+ coho smolts observed in 2004, 2005, and 2009 was used to estimate the number of coho smolts produced in 2009. This equation is expressed by y = 0.7532x + 0.1485 (Figure 20), where x is equal to 2+ steelhead efficiency and y is equal to 1+ coho efficiency. When marked 2+ steelhead were released but none were recaptured during the week, the seasonal trap efficiency of 19.87% was used to correlate trap efficiency for 1+ coho. Water temperature and flow monitoring Hourly water temperatures were recorded with an Onset Optic StowAway temperature logger attached to the downstream end of the trap (Figures 22, 23). Stream flow measurements presented in this report are preliminary data from the United States Geological Survey (USGS) stream gauge number 11517500, Shasta River, Yreka (SRY, Figure 21). This gauge is located approximately.75 miles upstream of the confluence with the Klamath River. Results The Shasta River rotary trap began sampling six days per week on February 11, 2009. Trapping ended after 20 weeks on July 1, 2009. The trap fished 120 sets for a total of 2,572.23 hours. An estimated 266,708,605.9 cubic feet of water were sampled. The number of salmonids trapped, marked and recaptured by week, and weekly population estimates with a 95% Confidence Interval (CI) are shown in Appendices 1-9. Weekly mean fork lengths, sample size, minimum and maximum size and standard deviations for Chinook, coho, and steelhead are shown in Appendices 18-26. Chinook 0+ An estimated 718,949 0+ Chinook (95% CI, 687,412 750,486) emigrated from the Shasta River during weeks 7 through 26. The greatest number of Chinook left during week 12 (112,832, 95% CI, 104,849 120,815). This is equal to 15.7% of the total estimate (Figures 1 and 2). The mean fork length for 0+ Chinook during week 12 was 44 mm (Appendix 18). Chinook 1+ An estimated 562 (95% CI, 303 821) 1+ Chinook emigrated from the Shasta River during weeks 8 through 19. The greatest number of 1+ Chinook left during week 15 (160, 95% CI, 1-338) (Appendix 2). This is equal to 28.5% of the total estimate. Seasonal trap efficiency of 22.09% was used to provide an estimate for Julian week 17 since no successful mark-recapture trial occurred. The mean fork length for 1+ Chinook during week 15 was 136 mm (Appendix 19). Figure 3 shows the average weekly fork lengths for 0+ and 1+ Chinook. Coho 0+ An estimated 5,423 0+ coho emigrated from the Shasta River during weeks 13 through 26 based on trap efficiencies compared to 0+ steelhead. The greatest number of coho, 1,364, left during week 20 (Figure 4). This is equal to 25.16% of the total estimate (Figure 5) and is based on the 0+ steelhead seasonal trap efficiency. Seasonal trap efficiency for 0+ steelhead (15.83%) was used to provide an estimate for 0+ coho during Julian weeks 12, 16, 17, and 20. During Julian weeks 13-15 and 18, 0+ coho 3

trap efficiency of 13.41% was derived from a correlation between 0+ steelhead and 0+ coho efficiencies (Figure 19). The mean fork length for 0+ coho during week 20 was 59 mm (Appendix 20). Coho 1+ An estimated 5,396 1+ coho emigrated from the Shasta River during weeks 8 through 24. The greatest number of coho, 2,110, left in week 16. This number is based on actual mark-recapture trials and is equal to 39.10% of the total estimate (Figure 6 and 7). The correlation between 1+ coho and 2+ steelhead trap efficiencies were used to provide an efficiency and population estimate for 1+ coho during Julian weeks 7, 13-15, and 18-22 (Figure 20). Seasonal trap efficiency for 2+ steelhead (28.63%) was used to provide a population estimate for Julian weeks 9 and 23. The mean fork length for 1+ coho during week 15 was 143 mm (Appendix 21). Coho 2+ A total of 98 2+ coho were trapped emigrating from the Shasta River during weeks 8 through 21. 94.89% of total trapped 2+ coho left during weeks 15 and 16 (Appendix 5). Due to limited mark/recapture trials for 2+ coho, we are unable to correlate efficiencies or provide an accurate population estimate for 2009. Figure 8 shows the average weekly fork lengths for 0+, 1+ and 2+ coho. Steelhead 0+ An estimated 5,255 0+ steelhead (95% CI, 4,160 6,350) emigrated from the Shasta River during weeks 13-15, 18-19 and 21-26. The greatest number left during week 25 (1,517, 95% CI, 997 2,038) (Figure 9). This is equal to 28.9% of the total estimate for the period sampled (Figure 10). Seasonal trap efficiency of 15.83% was used to provide an estimate for Julian weeks 13-15 and 18 since no successful mark-recapture trials occurred. The mean fork length for 0+ steelhead during week 25 was 69 mm (Appendix 23). Steelhead 1+ An estimated 1,980 1+ steelhead (95% CI, 1,557 2,403) emigrated from the Shasta River in weeks 8-26. The greatest number left during week 21 (388, 95% CI, 145 631) (Figure 11). This is equal to 19.6% of the total estimate for the period sampled (Figure 12). Seasonal trap efficiency of 24.18% was used to provide an estimate for Julian weeks 9-11, 15, 22-23, and 26 since no successful mark-recapture trials occurred. The mean fork length for 1+ steelhead during week 21 was 157 mm (Appendix 24). Figure 13 shows average weekly fork lengths for 0+ and 1+ steelhead. Steelhead 2+ An estimated 27,395 2+ steelhead (95% CI, 23,852 30,939) emigrated from the Shasta River during weeks 7 through 25. The greatest number left during week 16 (10,327, 95% CI, 8,601 12,053) (Figure 14). This is equal to 37.7% of the total estimate for the period sampled (Figure 15). Seasonal trap efficiency of 19.87% was used to provide an estimate for Julian weeks 9 and 23-25 since no successful markrecapture trials occurred. The mean fork length for 2+ steelhead during week 16 was 185 mm (Appendix 25). 4

Steelhead 3+ An estimated 2,689 3+ (95% CI, 1,768 3,610) emigrated from the Shasta River during weeks 8 17 and 19. The greatest number left during week 16 (1,307, 95% CI, 629 1,984) (Figure 16). This is equal to 48.6% of the total estimate for the period sampled (Figure 17). Seasonal trap efficiency of 10.12% was used to provide an estimate for Julian weeks 8, 10, 13, and 19 since no successful mark-recapture trial occurred. The mean fork length for 3+ steelhead during week 16 was 247 mm (Appendix 26). Figure 18 shows average weekly fork lengths for 2+ and 3+ steelhead. Temperature Monitoring The Maximum Weekly Maximum Temperature during the trapping period occurred in Julian week 26 when a temperature of 25.94 C was observed. The Maximum Weekly Average Temperature of 22.59 C also occurred in Julian week 26 (Appendix 35). Water temperatures recorded hourly with weekly mean, maximum, and minimum temperatures are shown in Figures 22 and 23, respectively. estimate Shasta River 2009, 0+ Chinook estimates weeks 7-26 estimate 718,949 (95% CI, 687,412-750,486) 140000 120000 100000 80000 60000 40000 20000 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 1 Shasta River 2009 0+ Chinook estimates weeks 7-26 5

percentage of total 16.00% Shasta River 2009 weekly 0+ Chinook estimates as percentage of total estimate 14.00% 12.00% 10.00% 8.00% 6.00% 4.00% 2.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 2 Shasta River 2009 0+ Chinook estimates as percentage of total mean fork length 160 Shasta River Chinook 2009, weekly mean fork lengths for 0+ and 1+ sampled with standard deviation 140 120 100 80 0+ 1+ 60 40 20 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 3 Shasta River 2009 weekly mean fork lengths for 0+ and 1+ Chinook sampled 6

estimate 1400 Shasta River 2009, 0+ coho estimates based on correlation between 0+ steelhead and 0+ coho efficiencies, weeks 7-26 estimate 5423 1200 1000 800 600 400 200 0 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 4 Shasta River 2009 0+ coho estimates weeks 7 26 percentage of total 30.00% Shasta River 2009 weekly 0+ Coho estimates as percentage of total estimate 25.00% 20.00% 15.00% 10.00% 5.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 5 Shasta River 2009 0+ coho estimates as percentage of total 7

Shasta River 2009, 1+ coho estimates based on correlation between 2+ steelhead and 1+ coho efficiencies, weeks 7-26 estimate 5396 estimate 2200 2000 1800 1600 1400 1200 1000 800 600 400 200 0 0 1 2 3 4 5 6 7 8 9 10111213141516171819202122232425262728 Julian week Figure 6 Shasta River 2009 1+ coho estimates weeks 7-26 percentage of total Shasta River 2009 weekly 1+ coho estimates as percentage of total estimate 40.00% 35.00% 30.00% 25.00% 20.00% 15.00% 10.00% 5.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 7 Shasta River 2009 1+ coho estimate as percentage of total 8

mean fork length 250 Shasta River coho 2009, weekly mean fork lengths for 0+, 1+ and 2+ sampled with standard deviation 200 150 0+ 1+ 2+ 100 50 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 8 Shasta River 2009 weekly mean fork lengths for 0+, 1+, and 2+ coho sampled estimate Shasta River 2009, 0+ steelhead estimates weeks 7-26 estimate 5,255 (95% CI, 4,160-6,350) 2500 2000 1500 1000 500 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 9 Shasta River 2009 0+ steelhead estimates weeks 7-26 9

percentage of total 30.00% Shasta River 2009 weekly 0+ steelhead estimates as percentage of total estimate 25.00% 20.00% 15.00% 10.00% 5.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 10 Shasta River 2009 0+ steelhead estimates as percentage of total estimate 700 Shasta River 2009, 1+ steelhead estimates weeks 7-26 estimate 1,980 (95% CI, 1,557-2,403) 600 500 400 300 200 100 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 11 Shasta River 2009 1+ steelhead estimates weeks 7-26 10

percentage of total Shasta River 2009 weekly 1+ steelhead estimates as percentage of total estimate 20.00% 18.00% 16.00% 14.00% 12.00% 10.00% 8.00% 6.00% 4.00% 2.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 12 Shasta River 2009 1+ steelhead estimates as percentage of total mean fork length Shasta River steelhead 2009, weekly mean fork lengths for 0+ and 1+ sampled with standard deviation 180 160 140 120 100 0+ 1+ 80 60 40 20 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 13 Shasta River 2009 weekly mean fork length for 0+ and 1+ steelhead sampled 11

estimate 13500 Shasta River 2009, 2+ steelhead estimates weeks 7-26 estimate 27,395 (95% CI, 23,852-30,939) 12000 10500 9000 7500 6000 4500 3000 1500 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 14 Shasta river 2009 2+ steelhead estimates weeks 7 26 percentage of total 40.00% Shasta River 2009 weekly 2+ steelhead estimates as percentage of total estimate 35.00% 30.00% 25.00% 20.00% 15.00% 10.00% 5.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 15 Shasta River 2009 2+ steelhead estimates as percentage of total 12

estimate 2000 Shasta River 2009, 3+ steelhead estimates weeks 7-26 estimate 2,689 (95% CI, 1,768-3,610) 1800 1600 1400 1200 1000 800 600 400 200 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 16 Shasta River 2009 3+ steelhead estimates weeks 7 26 percentage of total 50.00% Shasta River 2009 weekly 3+ steelhead estimates as percentage of total estimate 40.00% 30.00% 20.00% 10.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 17 Shasta River 2009 3+ steelhead estimates as percentage of total 13

mean fork length Shasta River steelhead 2009, weekly mean fork lengths for 2+ and 3+ sampled with standard deviation 450 400 350 300 250 2+ 3+ 200 150 100 50 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 18 Shasta River 2009 weekly mean fork lengths for 2+ and 3+ steelhead sampled 60.00% Shasta River 2005, 2006, 2008 correlations between 0+ coho and 0+ steelhead trap efficiencies for Julian weeks 20-27 y = 0.8224x + 0.0039 R 2 = 0.7795 coho 0+ trap efficiency 50.00% 40.00% 30.00% 20.00% 10.00% 0.00% 0.00% 10.00% 20.00% 30.00% 40.00% 50.00% 60.00% 70.00% 0+ steelhead trap efficiency Figure 19 Shasta River 2009 0+ coho/0+ steelhead efficiency correlations weeks 20-27 14

50.00% Shasta 2004, 2005, 2009 correlations between 1+ coho and 2+ steelhead trap efficiencies for weeks 14-19 y = 0.7532x + 0.1485 R 2 = 0.6479 1+ coho trap efficiency 40.00% 30.00% 20.00% 10.00% 0.00% 0.00% 5.00% 10.00% 15.00% 20.00% 25.00% 30.00% 35.00% 40.00% 2+ steelhead trap efficiency Figure 20 Shasta River 2009 1+ coho/2+ steelhead efficiency correlations cfs Shasta River 2009 flow by Julian week, recorded at 15 minute intervals, USGS Gauge # 11517500 300 250 200 150 100 50 0 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 21 Shasta River 2009 flow by week 15

C Shasta River 2009 water temperatures Recorded hourly at the rotary trap, Julian weeks 7-26 30 25 20 15 10 5 0 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 22 Shast a River 2009 water temperatures by week Shasta River 2009 weekly mean, maximum and minimum water temperatures recor ded at the rotary trap (lo gger #1289578) Cº 30 25 20 15 10 5 0 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week maximum mean minimum Figure 23 Shasta River 2009 weekly mean, maximum, and minimum water temperatures 16

Discussion Multi year estimates Annual estimates of the number of juvenile salmonids produced in the Shasta River began in 2000. The multi year estimates listed below are limited to years in which the methods and the period sampled are comparable. The age class presented for each species is the most common age at which smolts are produced. These estimates are presented here for the purpose of comparison and to identify trends in the population. Details of the trap operation and catch can be found in the individual annual reports. The estimates presented below were made using methods similar to those described in this report. 95% confidence intervals are available for the weekly estimates except for weeks when no marked fish were recovered. Estimates for these weeks were made by expanding the weekly catch by the seasonal trap efficiency. C hinook Annual estimates of the number of 0+ Chinook produced from the Shasta River for 2002-2009 are shown in Figure 24. The estimate of 718,949 for 2009 is the sixth largest in the eight years of trap operation shown in Table 1. Table 1. Shasta River weekly production estimates for 0+ Chinook, 2002-2009 Julian Week 2002 2003 2004 2005 2006 2007 2008 2009 6 --- --- --- --- --- --- --- --- 7 --- 13429 125190 14470 1358 35803 10790 4325 8 --- 97358 401988 13942 2545 40407 20178 50745 9 321719 144206 395915 26738 1427 20975 124925 77894 10 622634 143548 851550 50927 154 57729 109082 7729 11 521745 86911 249353 33513 2654 93418 193534 58276 12 410963 100881 107549 15256 1531 71841 128298 112832 13 363540 171099 46026 14719 475 35228 66500 72436 14 738380 55585 26906 36996 939 26158 48978 47558 15 148765 35821 64925 23114 1087 41542 28872 49827 16 148890 17697 51207 11409 3499 20847 46221 62195 17 23015 17879 25286 6693 1886 18986 47950 67316 18 24995 8626 48625 6265 4243 28892 37348 10433 19 74983 6520 23136 3134 9777 24774 33558 8912 20 62352 26573 9206 9729 32600 32279 59676 59298 21 22535 65501 25328 18746 1564 17974 7765 15681 22 7407 22235 18534 4443 5320 10172 1292 6813 23 15971 5616 9205 1921 6170 1365 6819 2325 24 1251 539 3401 1869 2261 1011 7762 1868 25 208 504 1609 968 2300 334 3237 1698 26 33 173 1138 847 1586 5740 787 27 4 116 ---- ---- 10 ---- ---- 28 ---- 38 -- -- ---- 3 -- -- ---- 29 ---- 48 -- -- ---- -- -- -- -- ---- total 3,509,388 1,020,905 2,486,076 295, 699 83,389 579,735 988,525 718,949 17

Chino ok 0+ estimates 4,000,000 3,500,000 3,000,000 2,500,000 2,000, 000 1,500, 000 1,000,000 500,000 Figure 0 Shasta Rive r 0+ Chino ok estimates 2002-2009 2002 2003 2004 2005 2006 2007 2008 2009 year 24 Shasta River 2002 2009 0+ Chinook estimates 18

Steelhead Individual annual estimate s for 1+ and 2+ steelhead w ere first possi ble beginning in 2004 with the development of age leng th cuto ffs (Appendix 37 and 38). Prior to 2004 we produced combined estimates f or 1+ and 2+ stee lhead. Annual estimates of the number o f 2+ steelhead produced from the Shasta River for 2004-2009 are shown in Fig ure 25. The estimate of 27,395 for 2009 is the fourth largest for the six years for wh ich 2+ estimates have been made (Table 2). Table 2. Shasta River weekly production estimates for 2+ steelhead, 2004-2009 Julian Week 2004 2005 2006 2007 2008 2009 7 ----- 4 22 9 14 45 8 ----- ----- 41 125 10 114 9 112 7 2 10 38 83 10 612 89 27 143 252 279 11 4,125 760 2 1,732 191 377 12 8,458 538 15 5,382 164 698 13 1,938 376 2 2,472 920 2806 14 5,962 1,043 6 2,626 1,901 1329 15 7,500 1,262 4 1,890 1,739 2989 16 15,893 763 94 2,616 857 10327 17 27,048 3,278 2,391 7,637 1,731 3511 18 8,886 5,648 17,136 4,541 1,177 798 19 6,120 4,015 6,930 19,421 2,017 1595 20 6,398 3,718 4,975 6,543 1,264 2134 21 1,195 2,289 187 449 82 219 22 1,291 278 276 722 18 66 23 704 119 105 57 7 14 24 36 33 31 82 ----- 2 25 150 17 251 28 ----- 9 26 ----- ----- 125 ----- 5 ----- 27 ----- ----- 1 ----- ----- ----- 28 ----- ----- ----- ----- ----- ----- TOTAL 96,426 24,235 32,621 56,483 12,386 27,395 19

total estimate 110,000 100,000 90,000 80,000 70,000 60,000 50,000 40,000 30,000 20,000 10,000 0 Shasta River 2004-2009 2+ steelhead population estimates 2004 2005 2006 2007 2008 2009 year Figure 25 Shasta River 2004 2009 2+ steelhead estimates Coho 2003 was the first year we conducted trap efficiency trials for 0+ and 1+ coho and the first year that weekly and annual estimate s were made. Weekly es timates for 2003 through 2009 are show n in Table 3; annual estimates are shown in Figure 26. Table 3, Shasta River weekly production estimates for 1+ coho, 2003-2009 Julian 2003 2004 2005 2006 2007 2008 2009 W eek 7 21 ----- ----- 60 ----- ----- ----- 8 60 7 9 14 ----- ----- 16 9 400 15 ----- ----- ----- 4 10 10 58 5 18 18 4 ----- 18 11 100 78 46 85 ----- ----- 20 12 386 135 25 55 12 ----- 66 13 2,262 54 128 120 15 24 381 14 2,937 261 117 173 326 40 306 15 739 417 218 15 146 63 1246 16 1,762 337 266 226 232 39 2110 17 845 368 539 6,699 289 21 681 18 950 98 222 2,048 63 14 144 19 274 4 ----- 1,104 53 0 287 20 224 7 3 202 12 4 75 21 29 ----- ----- ----- 4 0 21 22 4 ----- ----- 8 12 ----- 5 23 ----- ----- 3 7 8 ----- 10 24 ----- 14 107 ----- 4 ----- ----- 25 ----- ----- 129 ----- ----- ----- ----- 26 ----- ----- 224 ----- ----- ----- ----- 27 ----- ----- ----- ----- ----- ----- ----- 28 ----- ----- ----- ----- ----- ----- ----- TOTAL 11,052 1,799 2,054 10,833 1,178 209 5,396 20

total estimate 12000 Shasta River, 2003-2009 1+ coho Population Estimates 10000 8000 6000 4000 2000 0 2003 2004 2005 2006 2007 2008 2009 year Figure 26 Shasta River 2003 2009 1+ coho estimates Coho smolt production and smolt to adult survival Estimates of the number of smolts produced per returning adult from 2003 through 2010 is shown in Table 4. The average number of smolts per adult produced for these years is 18.38 smolts. The projected adult returns for 2010 through 2013 are shown in Table 4 using the average rate of return of 2.90%. Figure 26 shows the annual population estimates from 2003-2009. Brood year 2009 is the largest remaining cohort, producing 5,396 1+ coho smolts (Table 5). Table 4 Coho 1+ produced per returning adult Brood year Adults 1+ produced in Year Smolts per Adult 2001 291 11052 2003 37.98 2002 86 1799 2004 20.92 2003 187 2054 2005 10.98 2004 373 10833 2006 29.04 2005 69 1178 2007 17.07 2006 47 208 2008 4.43 2007 255 5396 2009 21.16 2008 31 169 2010 5.45 2009 9 165 2011 18.38 2010 156 2867 2012 18.38 Projected production in 2011 and 2012 based on the average production of 18.38, 1+ smolts produced per returning adult and grilse for brood years 2001 2008 21

Table 5 Coho 1+ to adult survival Brood year Adults Emigration year 1+ produced % return Adults returning in Brood year 2001 291 2003 11052 3.37% 373 2004 2002 86 2004 1799 3.84% 69 2005 2003 187 2005 2054 2.29% 47 2006 2004 373 2006 10833 2.35% 255 2007 2005 69 2007 1178 2.63% 31 2008 2006 47 2008 208 4.33% 9 2009 2007 255 2009 5396 2.90% 156 2010 2008 31 2010 169 2.90% 5 2011 2009 9 2011 165 2.90% 5 2012 2010 156 2012 2867 2.90% 83 2013 Projected 1+ estimate for 2011 and 2012 were made using the mean smolt produced per adult and grilse value (18.38%) from 2001 through 2008 Projected adult returns in 2010-2012 are based on the average 1+ smolt to adult survival rate for 2004-2008 (2.90%). Trap operation Even with afternoon and evening trap checks, heavy debris loading during weeks 18, 19, 20, 23 and 24 made it necessary to end a total of twelve sets by midnight. During these sets, large amounts of filamentous algae loaded the live car so quickly that it would have been necessary to tend the trap continuously to prevent fish mortalities. Sets were ended by raising the cone and bringing the trap to the bank. The catch was processed as usual in the morning. Scott River Rotary Screw Trap Summary Methods The Scott River was sampled with a five foot and an eight foot rotary screw trap manufactured by EG Solutions, Corvallis, Oregon. The traps were operated six days per week, Sunday afternoon through Saturday morning, at approximately 4.75 miles upstream of the confluence with the Klamath River at 041º 43' 34.87" N, 123º 00' 30.11" W. The catch in the trap was processed daily at approximately 0900 hours. Velocity of the water entering each cone was measured at the beginning and end of each set with a flow meter manufactured by General Oceanics model 2030R. Total volume sampled was calculated for each set. All vertebrates collected in the trap were identified and counted. Salmonids collected in the trap were classified by species, age and life stage. Scale samples and fork length data were collected from a random sample of salmonids in the catch. 22

Age Determination The same age length cutoffs for salmonids in 2007 were used in 2009. These cutoffs were determined from fork length frequency distributions and by estimating the age of scales in the 2001-2007 collection. Individual scale samples were visually examined and categorized into brood years using scale age-estimation methods (Van Oosten 1957, Chilton and Beamish 1982, Casselman 1983). Fork length intervals for each age class were determined for appropriate time periods and updated throughout the season. The Scott River coho cut off was in question and therefore the scales collected in 2009 were examined. After the scales were examined the existing cut off from 2007 was determined to be correct and remained unchanged. The intervals are not absolute and as a result of variable growth, some individuals may be larger or smaller than the cutoff fork length. The fork length cutoffs and the number of scales examined to determine the cutoffs are shown in Appendix 38. Trap Efficiency Determinations and Production Estimates Trap efficiencies for steelhead and Chinook were calculated weekly using the same methods described in the Shasta River section of this report on page 2. Due to the expected increase in smolt production from the return of 1,622 adult coho in 2007 (Knechtle 2008), we conducted weekly efficiency trials for 0 and 1+ coho. Changes in sampling equipment throughout the season made it necessary to calculate three separate seasonal trap efficiencies for each species in 2009. Early season trap efficiency was based on Julian weeks 7-11 when only the eight foot trap was fishing. Mid-season trap efficiency was based on Julian weeks 12-18 when both the five and eight foot trap were fishing. Late season trap efficiency was based on Julian weeks 20-26 when only the five foot trap was fishing in the former location of the eight foot trap. Due to the high flow event on 5/5, no estimates or trap efficiency were calculated for week 19. Water temperature and flow monitoring Hourly water temperatures were recorded with an Onset Optic StowAway temperature logger attached to the downstream end of the trap. Stream flow measurements presented in this report are made using preliminary data from the United States Geological Survey (USGS) recorded at stream gauge number 11519500 (Figure 38). This gauge is located approximately 19.5 miles upstream of the trap. Several large tributaries without stream gauges and numerous small streams enter the Scott River between the gauge and the trap and are not included in the flow measurements. Results The eight-foot Scott River rotary trap began sampling six days per week on February 11, 2009. This trap broke loose from its rigging during a high flow event on May 5, 2009; consequently, its final set for the season was on May 4, 2009. The trap fished 72 sets for a total of 1,597.33 hours. An estimated 143,021,086 cubic feet of water was sampled. The five-foot Scott River rotary trap began sampling six days per week on March 18, 2009. Trapping ended on July 1, 2009. The trap fished 76 sets for a 23

total of 1,736.95 hours. An estimated 192,967,802.9 cubic feet of water was sampled during the season. The number of fish trapped, marked and recaptured by week, and weekly estimates with 95% CI for all age classes of salmonids with population estimates are shown in Appendices 10-17. Weekly mean fork length, sample size, minimum and maximum size and standard deviation for each species and age class are shown in Appendices 27-34. Seasonal trap efficiencies Table 6 shows the seasonal trap efficiencies for all age classes of juvenile Chinook, coho and steelhead for three different time periods throughout the season. These time periods correspond to the use of different sampling equipment and events as described in the methods section of this report. Table 6. Scott River seasonal trap efficiencies by period and species and age class Seasonal Trap Efficiency Species Age Class Week 7-11 Weeks 12-18 Weeks 20-26 Chinook 0+ 3.76% 8.54% 3.87% 1+ 11.27% 18.52% ----- Coho 0+ ----- 16.67% 8.00% 1+ 6.24% 11.30% 5.65% Steelhead 0+ ----- 0.00% 1.10% 1+ 5.11% 10.02% 4.48% 2+ 3.49% 2.98% ----- 3+ 0.00% ----- ----- Chinook 0+ An estimated 930,731 0+ Chinook (95% CI, 876,028 985,433) emigrated from the Scott River during the period sampled. The greatest number of 0+ Chinook left during week 16 (275,700, 95% CI, 242,140 309,261) (Figure 27). This is equal to 29.6% of the total estimate (Figure 28).The mean fork length for 0+ Chinook during week 16 was 40 mm (Appendix 27). The seasonal trap efficiency was used to generate estimates for 0+ Chinook in Julian weeks 8 and 10 due to the absence of marked fish in the catch. Chinook 1+ An estimated 9,695 1+ Chinook (95% CI, 6,978 12,413) emigrated from the Scott River during weeks 7-16. The greatest number left during week 8 (2,738, 95% CI, 1,409 4,067). This is equal to 28.2% of the total estimate. Mid-season trap efficiency of 18.52% was used to provide an estimate for Julian week 17 since no successful mark-recapture trial occurred. The mean fork length for 1+ Chinook during week 8 was 92 mm (Appendix 28). Figure 29 shows the average weekly fork lengths for 0+ and 1+ Chinook. 24

Coho 0+ An estimated 3,899 0+ coho (95% CI, 3,061 4,736) emigrated from the Scott River during weeks 13 18 and 21-26. The greatest number left during week 17 (1,864 95% CI, 1,191 2,538) (Figure 30). This is equal to 47.8% of the total estimate (Figure 31). Mid-season trap efficiency of 16.67% was used to provide an estimate for Julian weeks 13-16 since no successful mark-recapture trial occurred. Late-season trap efficiency of 8.00% was used for Julian weeks 22 and 24. The mean fork length for 0+ coho during week 17 was 35 mm (Appendix 29). Coho 1+ An estimated 62,220 (95% CI, 54,277 70,163) 1+ coho emigrated from the Scott River during weeks 7 18. The greatest number left during week 10 (13,029, 95% CI, 7,770 18,287) (Figure 32). This is equal to 20.9% of the total estimate (Figure 33). Late-season trap efficiency of 5.56% was used to provide an estimate for Julian week 20-24 since no successful mark-recapture trial occurred. The mean fork length for 1+ coho during week 10 was 91 mm (Appendix 30). Figure 34 shows the average weekly fork lengths for 0+ and 1+ coho. Steelhead 0+ An estimated 919 0+ steelhead (95% CI, 20 1,817) emigrated from the Scott River during weeks 21 26. Week 26 is the only week when a successful mark-recapture trial occurred. Efficiency of 3.92% in this week may not be sufficient to create an accurate population estimate. The greatest number of steelhead was observed during week 25 (65 total trapped, Appendix 14). The mean fork length for 0+ steelhead during week 25 was 43 mm (Appendix 31). Steelhead 1+ An estimated 88,424 1+ steelhead (95% CI, 74,354 102,494) left the Scott River between weeks 7 through 26. The greatest number left during week 11 (21,208 95% CI, 11,720 30,696) (Figure 35). This is equal to 24% of the total estimate for the period sampled (Figure 36). Early-season trap efficiency of 5.11% was used to provide an estimate for Julian week 8 since no successful mark-recapture trial occurred. Late-season trap efficiency of 4.50% was used for Julian weeks 21 and 23-26. The mean fork length for 1+ steelhead during week 11 was 78 mm (Appendix 32). Figure 37 shows the average weekly fork lengths for 0+ and 1+ steelhead. Steelhead 2+ An estimated 8,334 2+ steelhead (95% CI, 4,325 12,342) left the Scott River in weeks 7 18. The greatest number left during week 16 (2,518 95% CI, 56 4,980) (Figure 38). This is equal to 30.2% of the total estimate for the period sampled (Figure 39). Early-season trap efficiency of 3.49% was used to provide an estimate for Julian weeks 7-8 and 10 since no successful mark-recapture trial occurred. Midseason trap efficiency of 2.98% was used for Julian weeks 17 and 18. The mean fork length for 2+ steelhead during week 16 was 128 mm (Appendix 33). Steelhead 3+ 25

A total of six 3+ steelhead were trapped in the Scott River in weeks 7, 8 and 15 (Appendix 17). Figure 40 shows the average weekly fork lengths for 2+ and 3+ steelhead. Temperature Monitoring The Maximum Weekly Maximum Temperature (average of daily maximum temperature for each week) of 22.93 C occurred in Julian week 26. The Maximum Weekly Average Temperature of 20.39 C also occurred in Julian week 26. (Appendix 36). Water temperature recorded hourly and mean, maximum, and minimum temperatures recorded weekly are expressed on figures 42 and 43 respectively. estimate Scott River 2009, 0+ Chinook estimates weeks 7-26 estimate 930,731 (95% CI, 876,028-985,433) 350,000 300,000 250,000 200,000 150,000 100,000 50,000 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 27 Scott River 2009 0+ Chinook estimates weeks 7-26 26

percentage of total Scott River 2009 weekly 0+ Chinook estimates as percentage of total estimate 30.00% 25.00% 20.00% 15.00% 10.00% 5.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 28 Scott River 2009 0+ Chinook estimates as percentage of total Scott River Chinook 2009, weekly mean fork lengths for 0+ and 1+ sampled with standard deviation mean fork length 140 120 100 0+ 1+ 80 60 40 20 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 29 Scott River 2009 weekly mean fork lengths for 0+ and 1+ Chinook sampled 27

estimate 3,000 Scott River 2009, 0+ coho estimates weeks 7-26 estimate 3,899 (95% CI, 3,061-4,736) 2,500 2,000 1,500 1,000 500 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 30 Scott River 2009 0+ coho estimates weeks 7 26 percentage of total Scott River 2009 weekly 0+ coho estimates as percentage of total estimate 60.00% 50.00% 40.00% 30.00% 20.00% 10.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 31 Scott River 2009 0+ coho estimates as percentage of total 28

estimate 20,000 18,000 16,000 14,000 12,000 10,000 8,000 6,000 4,000 2,000 0 Scott River 2009, 1+ coho estimates weeks 7-26 estimate 62,220 (95% CI 54,277-70,163) 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 32 Scott River 2009 1+ coho estimates weeks 7 26 percentage of total Scott River 2009, weekly 1+ coho estimates as percentage of total estimate 25.00% 20.00% 15.00% 10.00% 5.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 33 Scott River 2009 1+ coho estimates as percentage of total 29

fork length (mm) Scott River 2009, weekly mean forklength for coho 0+, 1+ sampled with standard deviation 140 120 100 80 60 0+ 1+ 40 20 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 34 Scott River 2009 weekly mean fork lengths for 0+ and 1+ coho sampled estimate 32,000 Scott River 2009, 1+ steelhead estimates weeks 7-26 estimate 88,424 (95% CI, 74,354-102,494) 28,000 24,000 20,000 16,000 12,000 8,000 4,000 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 35 Scott River 2009 1+ steelhead estimates weeks 7 26 30

percentage of total Scott River 2009 weekly 1+ steelhead estimates as percentage of total estimate 25.00% 20.00% 15.00% 10.00% 5.00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 36 Scott River 2009 1+ steelhead as percentage of total Scott River steelhead 2009, weekly mean fork length for 0+ and 1+ sampled with standard deviation fork length (mm) 180 160 140 120 100 80 1+ 0+ 60 40 20 0 0 5 10 15 20 25 30 Julian week Figure 37 Scott River 2009 weekly mean fork length for 0+ and 1+ steelhead sampled 31

estimate Scott River 2009, 2+ steelhead estimates weeks 7-26 estimate 8,334 (95% CI, 4,325-12,342) 5,400 4,800 4,200 3,600 3,000 2,400 1,800 1,200 600 0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week Figure 38 Scott River 2009 2+ steelhead estimates weeks 7-26 percentage of total 35.00% Scott River 2009 we ekly 2+ steelhead estimates as percentage of total estimate 30.00% 25.00% 20.00% 15.00% 10.00% 5. 00% 0.00% 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 39 Scott River 2009 2+ steelhead estimates as percentage of total 32

fork length (mm) 600 Scott River steelhead 2009, weekly mean fork length for 2+ and 3+ sampled with standard deviation 500 400 300 2+ 3+ 200 100 0 0 5 10 15 20 25 30 Julian week Figure 40 Scott River 2009 weekly mean fork lengths for 2+ and 3+ steelhead sampled cfs 4000 Scott River 2009 flow by Julian week, recorded at 15 min intervals, USGS gauge # 11519500 3000 2000 1000 0 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 41 Scott River 2009 flow by week 33

C Scott River 2009, water temperatures by Julian week, recorded hourly at the rotary screw trap (logger #1289596) + 30 25 20 15 10 5 0 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian Week No water temperature available in Julian week 19 due to loss of the trap and temperature logger. Figure 42 Scott River 2009 water temperatures by week Scott River 2009 weekly mean, maximum and minimum water temperatures C recorded at the rotary trap (logger #1289596) 30 25 20 15 10 5 maximum mean minimum 0 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Julian week No water temperat ure available injulian week 19 due to loss of the trap and temperature logger Figure 43 Scott River 2009 weekly mean, maximu m, and minimum water temperature 34

Discussion Due to low f lows, we were unable to fish the five foot trap during Julian weeks 7 through 11. B oth the five foot trap and the eight foot tra p were operating in Julian Week 12 (Figure 44). At 11:15 on 5/4/2009, flow at the USGS Scott River gauge was 685 CFS, by 11:15 on 5 /5/2009; the flow had increased t o 3,120 C FS at the gaug e. This sudden increase in flow separated the eight foot trap from its rigging. The eight foot trap drifted approximately.5 miles downstream to the first riffle below the trap site where the front harness fortunately wrapped on a large submerged rock (Photo 1). Photo 1 View from the deck of the 8 trap were it came to rest in the first riffle downstream of the sampling site. The trap broke loose from its rigging during the high flow event of 5/5/09. With the eight foot trap out of service, the five foot trap was moved to the eight foot trap site and resumed sampling on 5/13/09. Only one set was completed for Julian Week 19. For the remainder of the season, the five foot trap was the only trap in operation (Figure 44). 35

Days fished per week 7 Scott River 2009 Days and traps fished per week 6 5 4 3 5 foot trap 8 foot trap 2 1 0 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Julian week Figure 44 Scott River 2009 days traps fished per week Multi Year Estimates Chinook Annual estimates of the number of Chinook produced from the Scott River for 2004-2009 are shown in Figure 44. The estimate of 930,731 for 2009 is the second largest in the nine years of trap operation (Table 6). Table 6. Scott River weekly production estimates for 0+ Chinook, 2001-2009 Julian Week 2004 2005 2006 2007 2008 2009 7 5,481 ----- ----- 454 242 ----- 8 ----- ----- ----- 1,661 150 456 9 12,739 ----- ----- 710 3,477 ----- 10 47,188 2,027 936 5,293 32,328 394 11 83,499 9,898 54 418 10,634 8892 12 89,822 12,142 88 13,422 12,371 27839 13 137,491 3,936 52 10,690 30,274 74382 14 105,677 21,349 58 10,594 37,632 88192 15 92,404 14,631 32 26,439 79,632 173797 16 41,057 7,370 64 58,945 14,303 275700 17 26,080 4,316 ----- 12,274 32,757 82772 18 9,860 3,060 4 14,088 35,167 51991 19 16,935 3,987 53 5,154 20,304 ----- 20 7,739 4,171 ----- 12,732 5,197 37849 21 4,661 3,187 16 14,795 29,825 42249 22 5,650 6,006 24 3,838 52,534 12252 23 15,028 10,498 ----- 22,321 32,651 6014 24 44,100 3,894 16 51,526 33,061 11171 25 230,377 2,436 19 117,746 36,622 20068 26 50,803 16,578 2,624 52,180 53,310 16714 27 3,107 42,808 4,961 ----- ----- ----- 28 6,592 1,889 ----- ----- ----- TOTAL 1,029,696 178,885 10,890 435,279 552,472 930,731 36

total estimate 1,200,000 Scott River, 2001-2009 0+ Chinook Population Estimates 1,000,000 800,000 600,000 400,000 200,000 0 2001 2002 2003 2004 2005 2006 2007 2008 2009 year Figure 45 Scott River 2001 2009 0+ Chinook estimates Steelhead Annual estimates of the number of 2+ steelhead produced from the Scott River for 2004-2009 are shown in Figure 46. The estimate of 8,334 for 2009 is the fourth largest in the nine year s of trap operation. In 2004 only one efficiency trial in Julian week 16 was successful with a single recaptured fish. Table 7. Sco tt River weekly production estimates for 2+ steelhead, 2004-2009 Julian Week 2004 2005 2006 2007 2008 2009 7 3 82 120 309 68 31 8 3 79 110 104 17 99 9 3 744 64 ----- 560 608 10 22 1,270 99 2,016 949 736 11 12 1,788 6 2,283 1,990 61 12 8 1,114 253 12,642 468 375 13 5 1,588 510 4,946 1,213 1020 14 10 3,000 308 2,461 3,952 429 15 6 2,242 272 4,302 3,631 2423 16 23 4,988 6 1,554 616 2518 17 12 2,182 90 429 89 32 18 7 529 24 256 55 4 19 11 569 108 540 3 ----- 20 26 132 522 11,100 ----- ----- 21 23 51 3,519 2,875 8 ----- 22 21 242 592 782 22 ----- 23 21 1,353 210 86 6 ----- 24 22 1,426 255 61 22 ----- 25 10 175 15 28 4 ----- 26 6 41 112 35 0 ----- 27 4 1,457 434 ----- ----- ----- 28 ----- 5,022 ----- ----- ----- ----- TOTAL 258 30,074 7,629 46,810 13,671 8,334 37

Scott River, 2004-2009 2+ steelhead population estimates total estimate 50,000 45,000 40,000 35,000 30,000 25,000 20,000 15,000 10,000 5,000 0 2004 2005 2006 2007 2008 year 2009 Figure 46 Scott River 2004 2009 2+ steelhead estimates Coho W eekly estimates of the number of 1+ coho emigrating from the Scott River in 2003 and 2005 through 2009 are shown in Table 8. Figure 47 shows the annual population estimates for the same period. In 2004 there were no recaptures for either 2+ steelhead or 1+ coho and no estimate was possible (Table 9).. Scott River, 2003-2009 1+ Coho population estimates total estimate 80,000 70,000 60,000 50,000 40,000 30,000 20,000 10,000 0 2003 2004 2005 2006 2007 2008 2009 year Figure 47 Scott River 2003 2009 1+ coho population estimates 38

Table 8. Scott River weekly production estimates for 1+ coho, 2003-2009 Julian Week 2003 2004 2005 2006 2007 2008 2009 Multiyear Average 7 ----- ----- 6 ----- 22 11 476 164 8 ----- ----- 10 329 0 10 1558 477 9 489 ----- 27 558 11 5 4805 1,177 10 272 ----- 43 277 0 ----- 13029 3,405 11 2,367 ----- 162 1,230 11 37 12939 3,347 12 10,136 ----- 61 1,028 22 28 6510 3,552 13 1,677 ----- 91 2,914 89 55 6252 2,198 14 3,600 ----- 294 1,815 201 179 2866 1,751 15 4,068 ----- 268 2,166 458 109 4976 2,318 16 1,338 ----- 148 6,131 290 150 4389 2,431 17 1,261 ----- 181 6,107 190 108 2261 1,984 18 771 ----- 200 5,437 759 158 1553 1,624 19 506 ----- 48 9,935 893 5 ----- 2,623 20 3,967 ----- 100 4,148 357 16 437 1,734 21 800 ----- ----- 7,436 480 ----- 48 2,761 22 1,613 ----- 21 16,486 100 36 68 3,645 23 961 ----- ----- 2,548 33 17 47 893 24 312 ----- ----- 3,538 0 17 5 968 25 11 ----- ----- 1,875 11 2 ----- 629 26 ----- ----- ----- 1,072 ----- ----- 1,072 27 ----- ----- ----- 66 ----- ----- 66 28 ----- ----- ----- ----- ----- ----- ----- TOTAL 34,149 ----- 1,660 75,097 3,931 941 62,220 19,777 Table 9 Yearly mark-recapture totals and corresponding estimates for 1+ coho Scott River 1+ coho catch total marked released Recaptures population estimate 2003 1,412 1,004 25 34,149 2004 91 76 0 no estimate 2005 248 199 15 1,660 2006 3,828 2,980 185 75,097 2007 352 0 0 3,931 2008 160 114 11 941 2009 5,330 3,942 367 62,220 39

Acknowledgements The CDFG, Anadrom ous Fisheries Resource Assessment and Monitoring Program (AFRAMP) would like to acknowledge the people who contributed their efforts to a successful field season in 2009: Christopher Adams Luciano Chiaramonte Jack Herr Annie Horton Kristen Kirkby Denton Lopez Mark Pisano Donn Rehberg Steven Stenhouse Lou Uecker Joelle Vincent Thanks to the following agencies and organizations for their support: Shasta River Resource Conservation District AmeriCorps Watershed Stewards Project California Department of Fish and Game, Fisheries Restoration Grants Program Pacific States Marine Fisheries Commission Additional Thanks to: Bob Noyes of Gravity Works, for his excellent river safety training program and assistance 40