Chinook Salmon Populations for the Upper Sacramento River Basin In 2005

State of California The Resources Agency DEPARTMENT OF FISH AND GAME Chinook Salmon Populations for the Upper Sacramento River Basin In 2005 By Douglas Killam and Colleen Harvey-Arrison Northern California-North Coast Region Sacramento River Salmon and Steelhead Assessment Project SRSSAP Technical Report No. 06-3 2006

State of California The Resources Agency DEPARTMENT OF FISH AND GAME Chinook Salmon Populations for the Upper Sacramento River Basin 2005 1/ By Douglas Killam and Colleen Harvey-Arrison Northern California-North Coast Region Sacramento River Salmon and Steelhead Assessment Project SRSSAP Technical Report No. 06-3 2006 1/ This report is funded by the Sport Fish Restoration Act Grant F-51-R-18 Project 57. Some activities described in this report were through a cooperative investigation with the U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office and were supported by various funding sources including a CALFED ERP Grant as part of a cooperative agreement with the California Department of Fish and Game pursuant to the California Bay-Delta Environmental Enhancement and Water Security Act (PL. 104-333). Cover photo: Stream water turbulence in a riffle. SRSSAP photo ii

TABLE OF CONTENTS TABLE OF CONTENTS...iii TABLES AND FIGURES...iv SUMMARY...vii INTRODUCTION...1 METHODS and RESULTS...4 Carcass Mark and Recapture Surveys...4 Red Bluff Diversion Dam...5 Sacramento River Main-Stem Aerial Flight Redd Distribution...7 The 2005 Salmon Runs in the Upper Sacramento River Basin...8 Late-Fall-Run...8 Winter-Run...9 Spring-Run...10 Fall-Run...11 Tributary Specific Estimates...13 Clear Creek...13 Cow Creek...14 Cottonwood Creek...14 Battle Creek...14 Antelope Creek...15 Mill Creek...17 Deer Creek...20 ACKNOWLEDGEMENTS...23 LITERATURE CITED...25 APPENDIX A - Data Tables...26 APPENDIX B -Coded-Wire-Tag Results...37 APPENDIX C - Data Figures...43 iii

TABLES AND FIGURES TABLES Table 1. Summary of Chinook salmon population estimates for the USRB (Sacramento River System from Keswick Dam downstream to Princeton Ferry in 2005. Table 2. Summary of redd data collected from aerial flights for year 2005. APPENDIX A - Data Tables Appendix Table A1. Average migration timing for the various salmonid runs passing the Red Bluff Diversion Dam 1970-1988. Appendix Table A2. Summary of 2005 Red Bluff Diversion Dam fish passage information. Appendix Table A3. Summary of aerial redd counts for Sacramento River System from Keswick Dam downstream to Princeton from 1969-2005. Appendix Table A4. Summary of the 2005 carcass survey results for the main-stem Sacramento River salmon populations. Appendix Table A5. Summary of Chinook salmon population estimates by run in the Upper Sacramento River Basin, upstream of Princeton (RM 164) from 1986-2005. Appendix Table A6. Chinook salmon mark-and recovery data used to estimate the 2005 FRCS spawner population in Clear Creek from the former McCormick Saeltzer Dam sites to 6.4 km downstream, using the modified Schaefer equation. Appendix Table A7. Chinook salmon mark-and-recovery data used to estimate the 2005 FRCS spawner population in Battle Creek from Coleman NFH to the old hatchery site, using the modified Schaefer equation. Appendix, Table A8. Holding and spawning distribution of adult SRCS in Antelope Creek, 2005. Appendix, Table A9. Water temperature exceedence in Antelope Creek SRCS habitat, 2005. Appendix Table A10. Summary of SRCS counts in Antelope Creek by reach, 1983-2005. iv

Appendix Table A11. Spawning distribution of adult SRCS in Mill Creek, 2005. Appendix, Table A12. Water temperature exceedence in Mill Creek SRCS habitat, 2005. Appendix Table A13. Summary of SRCS redd counts and population estimates in Mill Creek, 1997-2005. Appendix Table A14. Chinook salmon mark-and-recovery data used to estimate the 2005 FRCS spawner population in Mill Creek from the Los Molinos Mutual Upper Diversion Dam downstream to the confluence with the Sacramento River, using the modified Schaefer equation. Appendix Table A15. Holding and spawning distribution of adult SRCS in Deer Creek, 2005. Appendix Table A16. Water temperature exceedence in Deer Creek SRCS habitat, 2005. Appendix Table A17. Summary of SRCS holding and spawning distribution and population counts in Deer Creek, 1992-2005. Appendix Table A18. Chinook salmon mark-and recovery data used to estimate the 2005 fall-run Chinook spawner population in Deer Creek from the USGS gauging station downstream to the Hwy 99 Bridge, using Chapman s version o f the Peterson equation. APPENDIX B - Coded Wire-Tag Results Tables Appendix Table B1. Summary of the Coded-wire-tag (CWT) results, by brood year, for adipose-fin clipped (hatchery) Chinook salmon in the Upper Sacramento River Basin in 2005 collected during Sacramento River Salmon and Steelhead Assessment Project escapement surveys. Appendix Table B2. Summary of the 2005 CWT results, by run, for adipose-fin clipped (hatchery) Chinook salmon in the Upper Sacramento River Basin collected during Sacramento River Salmon and Steelhead Assessment Project escapement surveys. Appendix Table B3. Summary of the 2005 CWT results, by hatchery, for adipose-fin clipped (hatchery) Chinook salmon in the Upper Sacramento River Basin collected during Sacramento River Salmon and Steelhead Assessment Project escapement surveys. v

Appendix Table B4. Summary of the 2005 CWT results, by tag code, for adipose-fin clipped (hatchery) Chinook salmon in the Upper Sacramento River Basin collected during Sacramento River Salmon and Steelhead Assessment Project escapement surveys. FIGURES Figure 1. The Upper Sacramento River Basin from Keswick Dam to Princeton. Figure 2. Antelope Creek, Tehama County, adult SRCS holding and spawning habitat. Figure 3. Mill Creek, Tehama County, adult SRCS holding and spawning habitat. Figure 4. Deer Creek, Tehama County, adult SRCS holding and spawning habitat. APPENDIX C Data Figures Appendix Figure C1. Average daily water temperature and salmon tolerance limits in Antelope Creek SRCS habitat, 2005. Appendix Figure C2. Average daily flow and adult SRCS migration timing in Mill Creek, March June, 2005. Appendix Figure C3. Average daily water temperature and migration tolerance limits during adult SRCS migration in Mill Creek, March June, 2006. Appendix Figure C4. Average daily water temperature and salmon tolerance limits in Mill Creek SRCS habitat, May October, 2005. Appendix Figure C5. Average daily flow and water temperature in Mill Creek during FRCS spawning, October December, 2005. Appendix Figure C6. Average daily flow, water temperature and tolerance limits during adult SRCS migration in Deer Creek, April June, 2005. Appendix Figure C7. Average daily water temperature and tolerance limits in Deer Creek adult SRCS habitat, May October, 2006. Appendix Figure C8. Average daily water flow, temperature and tolerance limits in Deer Creek during FRCS spawning, October December, 2005. vi

SUMMARY Population sizes were estimated for Chinook salmon passing upstream of Princeton Ferry in the Upper Sacramento River Basin (Figure 1). Annual population estimates for the Basin are determined through a number of methodologies including: carcass surveys, hatchery counts, aerial and instream redd surveys, snorkel counts, angler interviews, video counts and ladder counts at hatcheries and the Red Bluff Diversion Dam (RBDD). This report does not include salmon information from tributaries that enter into the Sacramento River downstream of Princeton Ferry (Butte Creek, and the Feather and American River(s)) or from Big Chico Creek near Chico. These and other waterways are detailed in reports from other projects. A summary of the entire California Central Valley salmon stocks is available annually in reports titled Annual Report: Chinook Salmon Spawning Stocks in California s Central Valley An estimated 311,683 Chinook salmon (salmon) were in the Upper Sacramento River Basin (USRB) upstream of Princeton Ferry in 2005. This includes an estimate of 19,777 late-fall-run, 15,839 winter-run, 3,697 spring-run, (SRCS) and 272,371 fall-run Chinook salmon, (FRCS) (Table 1). The majority of these salmon passed above RBDD (91%) to spawn in the tributaries or main-stem of the Sacramento River upstream of Red Bluff. Readers interested in conducting independent analysis of the data provided in this report should be aware that the summaries of data herein may be generalized to fit the limited scope of the report. For analytical data needs readers should directly contact the authors or other Project staff for specific requirements or limitations to the data. The authors may be reached via e-mail at (dkillam@dfg.ca.gov) or (charvey@dfg.ca.gov). This program received financial assistance through the Federal Aid in Sport Fish Restoration Act. The U.S. Department of the Interior prohibits discrimination on the basis of race, color, national origin, age, sex, or disability. If you believe you have been discriminated against in any program, activity, or facility, or if you desire further information, please write to: The Office of Human Resources U.S. Fish and Wildlife Service 4040 N. Fairfax Drive, Room 300 Arlington, CA 22203 vii

INTRODUCTION The Upper Sacramento River Basin (USRB) of California s Central Valley is unique in that it has four separate runs of Chinook salmon (Oncorhynchus tshawytscha) each year. Each run of Chinook salmon, hereafter referred to as salmon or run, (i.e. winter-run) has adopted a different life history (spawning locations, and seasonal timing) that allows it to survive the many different environmental conditions found over the course of a year in the USRB (the anadromous portions of the Sacramento River watershed upstream of Princeton CA) (Figure 1). Management of salmon stocks for both sport and commercial fisheries was the primary purpose for monitoring salmon stocks in the USRB for earlier years. (Note: the USRB has no spawning populations of other Pacific salmon species (Chum, Coho, Sockeye, Pink) other than Chinook and steelhead (O. mykiss)). In recent years the focus of monitoring has been augmented to provide feedback for restoration activities (including protection of listed stocks) in the Central Valley as well as the traditional role of managing stocks for sport and commercial fisheries. This report provides a summary of the monitoring activities for salmon populations that occurred in 2005 in the USRB. The data found here is a compilation of the many different sources and methodologies used to produce population estimates within the USRB. Annual reports providing data on the USRB salmon populations are available going back to the early 1950 s. In these early years, data is often lacking for particular streams due to lack of funding and personnel. Fish ladders and hatchery counts were the primary methods of data collection until 1967. From 1967 until 1986 the Red Bluff Diversion Dam (RBDD) provided a method of monitoring the four salmon runs as well as steelhead. During this period the RBDD was typically operated throughout the year allowing for complete accounting of escapement. Beginning in 1987, operation of the RBDD was restricted to facilitate improved passage of winter-run salmon which were at critically low and declining population levels and had been previously petitioned for listing (October 1985) under state and federal Endangered Species Act (ESA). From 1995 to present day, the RBDD has been operated from approximately 15 May through 15 September. The data produced at the RBDD has largely been replaced by carcass survey data but the RBDD is still utilized to provide some data for the USRB. Carcass surveys using mark and recapture methodologies were initiated in 1996 on the main-stem Sacramento River above RBDD. The year-round main-stem carcass surveys now provide the only source of natural spawning late fall-run escapement in the USRB, as well as report the fall and winter-run escapements used by the Department of Fish and Game (Department) as official estimates. 1

Figure 1. The Upper Sacramento River Basin (from Keswick Dam to Princeton Ferry). 2

Table 1. Summary of Chinook salmon population estimates for the USRB (Sacramento River System from Keswick Dam downstream to Princeton Ferry) in 2005. LOCATION Late-Fall-Run Winter-run* Spring-Run + Fall-Run Red Bluff up to Keswick Dam Sacramento River Main-Stem 9,565 15,730 0 44,950 Livingston Stone Hatchery 0 109 0 0 Battle Creek Coleman Hatchery 6,435 0 0 144,739 Battle Creek Above hatchery n/a^ 80 n/a Battle Creek Below Hatchery n/a 20,520 Clear Creek n/a 69 14,824 Cottonwood Creek n/a 47 n/a Angler Harvest (avg-1998-2002 ) vs run size 1,373 0 0 11,517 SUB-TOTAL UPSTREAM OF RBDD 17,373 15,839 196 236,550 Red Bluff down to Princeton Sacramento River Main-Stem 1,035 0 30 12,062 Mill Creek n/a 1,150 2,426 Deer Creek n/a 2,239 946 Antelope Creek n/a 82 n/a Angler Harvest (avg-1998-2002 ) vs run size 1,368 0 0 20,386 SUB-TOTAL DOWNSTREAM OF RBDD 2,403 0 3,501 35,820 SYSTEM GRAND TOTAL 19,777 15,839 3,697 272,371 (Keswick Dam to Princeton) 2005 TOTAL SALMON ALL RUNS COMBINED: 311,683 NOTE: These values represent minimum numbers, unsurveyed waters have additional smaller salmon populations * Carcass survey results vs RBDD of 5,299. + Battle and Clear Creek number(s) are draft data pending results of Spring-run genetic testing and reporting by USFWS ^ n/a: Is not available, represents salmon present but no estimate available. The CALFED-funded Sacramento River Winter-run Chinook carcass survey has provided the official escapement estimate for this federally and state-listed endangered species since 2001 (Killam, 06-2, 2006). This species currently spawns only in the mainstem Sacramento River and is the focus of many restoration activities throughout the Central Valley. This estimate forms the scientific basis for establishing allowable take limits at the pumping facilities in the Delta. Fall-run salmon inventories have been routinely conducted since 1953 on USRB tributary streams. Prior to 1988, Peterson mark/recapture methodologies, ladder counts and aerial redd surveys were used with varying sampling intensity and reliability of estimates. Since 1988, mark/recapture surveys have been standardized into weekly surveys for the duration of the spawning run on each tributary. The mark/recapture estimator used on each creek (seasonal Peterson, Schaefer or Jolly-Seber), is based on the total carcasses encountered and weekly percent recovery of tags. In Battle Creek, a video counting station was operated (third year) to compare carcass mark/recapture estimates with real time immigration monitoring, Killam, 06-1 2006.. 3

Spring-run salmon inventories have been sporadically conducted since the 1940 s on USRB tributary streams. Methodologies from the 1940 s through the 1980 s were incomplete, inconsistent and not reproducible at best. In many years surveys were not conducted. Spawning escapement estimates were derived from incomplete spawning ground surveys, carcass surveys with unknown expansion factors, and partial ladder and weir counts. Since the early 1990 s, in a effort to standardize sampling efforts and develop an annual index of abundance, a single escapement estimator has been selected for each spring run tributary, recognizing the sampling limitations in each watershed. Unlike fall-run carcasses surveys, too few spring run carcasses are encountered to obtain a percent recovery for a tag/recapture escapement estimator. In Deer, Antelope and Beegum Creek(s) a snorkel survey of the known holding habitat is conducted to obtain an annual count of holding salmon. In Mill Creek water clarity prohibits reliable underwater observation, consequently an annual redd survey is conducted and expanded into a population estimate. Late-fall-run salmon carcass surveys are difficult to conduct on USBR tributaries due to high flow conditions, making consistent weekly mark-recapture surveys not practical. Late-fall-run salmon are known to spawn in most fall-run tributaries and opportunities for alternative monitoring opportunities exist but at present only Clear Creek (United States Fish and Wildlife Service-USFWS-carcass count) and Battle Creek (hatchery count- USFWS) provide salmon data (counts). The late-fall-run escapement on the Sacramento River is monitored through a mark-recapture carcass survey and aerial redd counts. METHODS and RESULTS Since 1969 the RBDD estimates were used to generate estimates for all runs of salmonids in the Sacramento River (steelhead, four runs of Chinook salmon). In 2005 only the RBDD data from spring-run salmon were used in the official estimate. To provide continued RBDD data trends, estimates using the RBDD data are still generated but the Department has used carcass surveying as the means for generating official estimates since 2001. Carcass Mark and Recapture Surveys: Carcass mark and recapture surveys (carcass surveys) have been used by the Department for many years to estimate salmon populations on rivers throughout the state. Since all Chinook salmon die after spawning a population can be counted by estimating how many carcasses were present each year. Because of the current gates out schedule at the RBDD (September- May) the carcass surveys have been chosen as the official alternative to the RBDD count for the Upper Sacramento River main-stem. Carcass surveys are conducted by boat or walking on foot along a river or stream examining carcasses. Carcasses are tagged with a colored plastic or some other type tag to enable personnel to recognize them on subsequent surveys. Carcasses that were tagged in previous periods and recaptured in new periods form the basic proportion of carcasses tagged to carcasses recaptured that create a population estimate. Data is often 4

collected on sex, length, hatchery origin salmon (in Appendix B), location, and other categories of interest. There are different methods or models employed to create an estimate. The Population models were created for live populations of organisms and each model has a list of sampling assumptions that must be met in order for the model to reflect an accurate portrayal of the population size. The three models used by the Department in the USRB are the Peterson, the Schaefer, and the Jolly-Seber. Each has been modified from the original intent of studying live organisms and applied to carcasses. Carcass surveys do not meet the underlying assumptions of any single model so it is often left up to the biologist analyzing the data as to which model best fits the data for a particular survey. Each model has numerous advantages and disadvantages. The Peterson model is the simplest and is useful in developing an estimate when disruptions to the sampling schedule occur. The Peterson takes the entire schedule and treats it as two periods, a tagging period and a recapture period. This is the least accurate model but is in some surveys the only one that can be used due to low numbers of recaptures, or floods, etc. The Schaefer and the Jolly-Seber models are more complicated and depend on repetitive survey periods and recaptured carcasses throughout the survey. Of the two the Jolly- Seber is the more complicated to analyze but recent software programs have been developed to allow calculation of this method. The Jolly-Seber differs from the Schaefer in that it attempts to account for survival of carcasses between survey periods. Historically, the Schaefer is utilized for the fall-run on tributaries on Battle and Clear Creeks. In 2001 the Jolly-Seber method was chosen as the method to be utilized whenever possible for the main-stem Sacramento River (winter, fall, and late-fall runs). Red Bluff Diversion Dam (RBDD): Estimates from the RBDD during 2005 were based on daily ladder counts made by the USFWS-Red Bluff Fish and Wildlife Office and by the fish-trap sampling conducted by the Department at the dam (late-fall-run excluded). Ladder counts were obtained through closed-circuit television monitoring of salmon passing through the RBDD fishways. Total counts of salmon passing each week were adjusted for those periods when the fishways remained open but no counts were possible, such as when river turbidity was high, during flood conditions when the dam gates were temporarily opened, and when no observations were made at night. Adjustments to lapses in daytime counts were made by interpolation. Night passage numbers were calculated by multiplying the 14-hour day ladder count by a "night-factor" which was generated from a twice-a-week night count. The adjusted weekly number of fish was apportioned among the winter-, spring-, and fall-runs based on their relative proportions seen that week in random samples of salmon taken from the dam's east-bank trapping facility. At the trap each salmon observed was assigned to a run based on phenotypical characteristics including: color, scale condition, and relative degree of sexual maturation (an indication of when it was believed that it would spawn). 5

Estimated numbers of salmon for those periods when the fish ladders were not operated (September-May) were calculated based on historical data. This historical data is presented as weekly averages for each run s migration past RBDD, and is provided in Appendix Table A1. The values presented in Appendix Table A1 are based on years when the RBDD gates were down throughout the year and the trap and fish ladders were operated continuously. Concern for declining populations of winter-run salmon resulted in the gates being raised for portions of each year. The data that was used to develop historic run timing is different for winter-run than the other runs. Spring-, late-fall- and fall-run weekly migration patterns are based on data from 1970 to 1988 (1986 for latefall). For the winter-run, 1982-1986 was chosen to be the historical average framework due to the reduced numbers of winter-run seen at RBDD during these years as more closely mirroring the current winter-run populations. The majority (average approx. 85%, 76%) of winter and fall-run migration occurs outside the season of the RBDD operation. The accuracy of spawner estimates based on the RBDD fish ladder counts are, therefore, highly suspect, and often result in estimates of negative numbers of fall-run salmon in the main-stem Sacramento River after known tributary estimates are subtracted from the RBDD estimate. The total for the 2005 salmon population estimates passing RBDD was calculated as follows: 1) For each Julian week, (Sunday-Saturday), determine estimate of actual salmon counted for period when gates were down (actual fish seen passing ladders + night and other adjustments = Estimate). (Other adjustments may include missing day counts, ad-clipped fish, and individual ladder closures.) 2) Determine from the RBDD trap data the percent of that week s passage to be assigned to a particular run (i.e., 75% winter-, 15% spring-, and 10% fall-run). 3) Determine the total number of salmon for each run during each week that actual counts were made. (Example: estimate multiplied by percentage in #2 for each run.) 4) Sum all of the weekly numbers of salmon counted for each run when counts were made and sum all of the corresponding percentages for those same weeks in Appendix Table A1. This provides the starting point to back calculate for period when the gates were up. 5) Calculate a total estimate for each run for the entire year using the proportion determined in step 4. (Example: winter-run 2005 total fish counted = 702, sum of historical percent during weeks of actual counts = 13.25%, thus total winter-run estimate is 702 * 100% /13.25% = 5,299 fish). 6) The RBDD data for 2005 is presented in Appendix Table A2. If desired, any week or months passage may be estimated by determining total historical passage for that period multiplied by the total in #5 for a given run of salmonids. 6

7) It is important to note that data from the RBDD does not account for downstream populations. These are determined through aerial redd counts. The data collected at the RBDD does not determine distribution and numbers into the tributaries and main-stem upstream of RBDD. Instead, the Department with seasonal assistance from the USFWS now conduct combinations of mark and recapture carcass surveys, aerial and in-stream redd surveys, hatchery counts, angler harvest surveys, weir counts, and snorkel surveys of the main-stem Sacramento River and the major salmon tributaries to determine adult salmon escapements for specific runs and streams. Sacramento River Main-Stem Aerial Flight Redd Distribution: In 2005, a Department airplane was used to conduct monthly surveys for the late-fall, spring and fall-run redd distributions. During the winter-run migration period a helicopter survey was conducted weekly to enable detailed inspection of winter-run spawning areas. Aerial redd maps are created (digital versions available) to document the location of spawning distributions in the main-stem and are used to supplement other counting methods to determine the overall population estimate for each run of salmon. Table 2 presents the data from the aerial redd surveys conducted by the Department. These surveys provide a historical database on redd distribution in the main-stem Sacramento River from Princeton (river mile (RM) 164) to Keswick Dam (RM 302) (1969-2005), Appendix Table A3. The surveys are also used to estimate spawning escapement in the main-stem downstream of RBDD or the carcass survey areas. Aerial flights are used to determine estimates downstream of carcass surveys or the RBDD for salmon spawning in the main-stem. A simple proportion is used to calculate this estimate. The proportion is constructed as follows: Number of salmon downstream = (salmon upstream after harvest in main-stem / redds upstream) * redds downstream. The Department conducted 22 aerial redd flights for the 2005 escapement surveys. Three late-fall-run surveys were conducted between 16 December 2004 and 15 March, (one was discounted due to fog hindering counting). A fourth late-fall flight was conducted on 15 December but those results are associated with the 2006 late-fall estimate. The majority of late-fall-run redds were from the Anderson Cottonwood Irrigation District Dam (ACID) upstream to Keswick Dam (47%). Eleven winter-run flights using a helicopter from 21 April through 3 August were flown. Winter-run redds were observed from Keswick Dam to just downstream of Deschutes Road Bridge near Anderson (RM 281). The majority of these redds (88%) were located between Keswick Dam and the Highway 44 Bridge in Redding. Five spring-run flights were conducted between 29 August and 30 September. A total of 105 redds were observed from Keswick Dam to just below the RBDD. Three fall-run flights between 25 October and 21 November reported fall-run redds from the Princeton Ferry site upstream to Keswick Dam. The fall-run redds were fairly evenly distributed with the majority (26.8%) observed from Keswick Dam downstream to the ACID Dam. 7

In summary, during 2005 there were 3,526 new redds observed in the main-stem from Keswick Dam to Princeton Ferry (RM 164) over a total of 22 flights. The majority of these redds (91%) were upstream of Red Bluff Diversion Dam. Appendix Table A3 presents a summary of historical aerial redd information for years 1969-2005. Table 2. Summary of redd data collected from aerial flights for year 2005. 2005 Summary of Aerial Redd Survey Data** Winter % Dist. Spring % Dist. Fall % Dist Late-Fall~ % Dist ALL % Dist. RIVER SECTIONS 1,029 52.3% 19 18.1% 324 26.8% 101 46.98% 1,473 41.8% Keswick to A.C.I.D. Dam. 701 35.6% 12 11.4% 42 3.5% 10 4.65% 765 21.7% A.C.I.D. Dam to Highway 44 Bridge 234 11.9% 42 40.0% 109 9.0% 1 0.47% 386 10.9% Highway 44 Br. to Airport Rd. Br. 4 0.2% 6 5.7% 207 17.1% 19 8.84% 236 6.7% Airport Rd. Br. to Balls Ferry Br. 0 0.0% 7 6.7% 118 9.8% 33 15.35% 158 4.5% Balls Ferry Br. to Battle Creek. 0 0.0% 2 1.9% 102 8.4% 22 10.23% 126 3.6% Battle Creek to Jellys Ferry Br. 0 0.0% 1 1.0% 42 3.5% 8 3.72% 51 1.4% Jellys Ferry Br. to Bend Bridge 0 0.0% 0 0.0% 10 0.8% 0 0.00% 10 0.3% Bend Bridge to Red Bluff Diversion Dam 0 0.0% 16 15.2% 178 14.7% 10 4.65% 232 6.6% Red Bluff Diversion Dam to Tehama Br. 0 0.0% 0 0.0% 49 4.0% 0 0.00% 49 1.4% Tehama Br. To Woodson Bridge 0 0.0% 0 0 15 1.2% 11 5.12% 26 0.7% Woodson Bridge to Hamilton City Br. 0 0.0% 0 0 13 1.1% 0 0.00% 13 0.4% Hamilton City Bridge to Ord Ferry Br. 0 0.0% 0 0 1 0.1% 0 0.00% 1 0.0% Ord Ferry Br. To Princeton Ferry. 1,968 100.0% 105 100.0% 1,210 100.0% 215 100.0% 3,526 100.0% ** Summary of 11 winter-run, 5 spring-run, 3 fall-run and 2 late-fall run flights ~ Late-fall run redd counts do not include survey on 1 March 2005 The 2005 Salmon Runs in the Upper Sacramento River Basin Late-fall-run: No estimates were made for the late-fall-run at the RBDD. Although some late-fall salmon use tributaries to the upper Sacramento River (e.g., Clear, Cow and Battle creeks) no spawner population estimates were made in those streams for late-fall salmon. The USFWS conducted a survey to tally carcasses, live fish and redds on Clear Creek latefall-run salmon, but no population estimate was generated. Of special note on late-fall salmon is that they spawn over the calendar year change. For the purposes of reporting late-fall numbers it is customary to report estimates based on when the juveniles emerge. Late-fall salmon spawning in November and December are classified as belonging to the following year, (i.e., December of 2004 spawners are put into 2005 estimate and December of 2005 spawners will be part of the 2006 estimate). A main-stem carcass survey was conducted from 14 December 2004 through 6 May 2005. These surveys covered a 21 km (13.2 mi) section of the Sacramento River between Keswick Dam, (RM 302), and the power lines just downstream of the mouth of Clear Creek (RM 288.8). The Jolly-Seber mark-and-recapture model estimated that 10,601 late-fall-run spawned in the Upper Sacramento River in 2005. This was based on a total of 1,473 examined adult female carcasses of which 590 were tagged and 279 subsequently recovered (47.3%-recovery rate). All fresh fish (n = 630) were measured and a grilse (2 year old) percentage of 11.9% was estimated based on a length of less than 610 millimeters. Males represented 55.5% of the population. Females were checked for egg retention following spawning. Only 19 of 361 fresh females (5.3%) had not completely spawned. All fish examined were checked for adipose fin clips representing 8

hatchery origin from the Coleman National Fish Hatchery (CNFH) on Battle Creek. A total of 168 of the salmon examined had an adipose (or unknown adipose) fin clip in 2005. Coded wire tags (CWT) were recovered from 149 of these and represented latefall, fall (n = 2) and winter-run salmon (n = 9) from CNFH and Livingston Stone National Fish Hatcheries (LSNFH). The two fall-run fish were from the Mokelumne River Fish Installation. The Jolly-Seber estimate is based on only the female adults from the carcass survey. Other fish including ad-clips, adult males, and grilse (jills, jacks) were accounted for using a combination of carcass survey results (ad-clips, grilse) and Keswick Dam trap sex ratios (adult males). Appendix Table A4 presents results of the main-stem carcass surveys and adjustments resulting in the 2005 late-fall-run (as well as winter and fallruns) estimate. The estimate of 10,601 also included an adjustment for the 41% of the aerial redds that were observed downstream of the carcass survey area. The late-fall-run are subject to sport fishing in the main-stem river below Deschutes Road Bridge (RM 280.9) The Department s Angler Harvest Survey was discontinued in July of 2003 so an average estimated harvest of late-fall salmon above Knights Landing in late 2004 and early 2005 was calculated to be 2,741 fish, (1,373 upstream RBDD). This estimate includes half of November s 2004 harvest (other half is considered fall-run) and all of December 2004 and of January 2005 and is developed by using the historical Angler Survey data. This total is not indexed to the spawning escapement size due to lack of data and would not include those late-fall fish harvested in November-December of 2005 as those fish are classified as year 2006 fish for the purposes of this report. The CNFH spawned and excessed late-fall salmon from December 2004 through March 2005. The hatchery total was 6,435 late-fall spawned and excessed, (includes 77 fish removed at Keswick trap), (Robert Null, USFWS, personal communication). Based on the carcass survey, angler survey, CNFH, and aerial redd data it is estimated that at least 19,777 late-fall-run salmon were present above Knights Landing in late 2004 and early 2005 (Table 1). This estimate does not include other in-stream tributary estimates that were not conducted due to limited staffing and typically poor weather and turbidity conditions during late autumn and winter. Winter-run: The Carcass Survey: A mark-and-recapture carcass survey for winter-run salmon was conducted on the Upper Sacramento River from 28 April through 2 September 2005 (Appendix Table A4). Based on a sample size of 3,476 tagged adult female carcasses and a recovery rate of 66.7% of these carcasses, a population estimate of 15,839 winterrun salmon was obtained using the Jolly-Seber model, (Killam, 06-2, 2006). The carcass survey results were based upon large (>609 mm) female carcasses. The number of spawning females (including grilse (42) and females retained at Livingston Stone National Fish Hatchery (56)) was 9,103. 9

Run size estimates at the RBDD have been made since 1967. The National Marine Fisheries Service (NMFS, 1996) developed draft winter-run population recovery goals of 10,000 spawning females over 13 consecutive years. This recovery goal was set using the RBDD winter-run population estimates. Beginning in 2001, the Department has chosen for regulatory purposes that the population estimates from the carcass survey will be used in reporting the winter-run salmon estimate. Data are still presented for the RBDD to continue trend data that has been available over the past 34 years. Red Bluff Diversion Dam: The RBDD estimate for the 2005 winter-run was 5,299. This included and estimated 4,263 natural-origin salmon (all hatchery winter-run have adipose fin-clipped off) and 1,036 hatchery-origin winter-run. Winter-run fish migrate past RBDD from December through August. Winter-run passing RBDD in December of 2004 were part of the 2005 estimate based on traditional run timing (Appendix Table A1). Most of these fish were thought to have spawned in the main-stem of the Sacramento River above Red Bluff. The Livingston Stone National Fish Hatchery (LSNFH) collected 109 winter-run for the LSNFH brood stock program). Other Winter-run Data: Eleven helicopter surveys were conducted to determine winterrun spawning distributions in the main-stem Sacramento River from Woodson Bridge (RM 218) to Keswick Dam (RM 302). This data is presented in Table 2. The proportion of redds above and below RBDD and the total estimate of winter-run passing RBDD are used to calculate the winter-run estimate for downstream of RBDD. In 2005, no winterrun redds were spotted downstream of RBDD during aerial flights. Therefore, the winterrun population estimate downstream of RBDD is 0 fish. There was no estimated angler harvest of winter-run above or below RBDD due to a zero salmon possession limit from 15 January through 16 July 2005 although some angling activities in late December and January in Delta probably catch winter-run. Also poaching and possibly hooking mortality associated with trout angling probably occurs. In summary, the official carcass survey reported 15,839 winter-run salmon (Table 1), while the historical RBDD winter-run estimate was 5,299 winter-run salmon in the Sacramento River in 2005. Spring-run: Spawning of natural spring-run in the Upper Sacramento River is considered by the Department to have largely been eliminated through competition plus hybridization with fall-run salmon (Department, 1998). Historically spring-run salmon migrated upstream in the late spring or early summer and held over the summer in higher elevations with cooler water temperatures. These fish were then spatially separated from the later arriving fall-run by low flows and warmer temperatures in the lower sections of the waterways. Presently, dams on the Sacramento River, Clear, and Battle creek(s) prevent the spring-run from being spatially isolated from the fall-run. Since fall and spring-run salmon are spawning around the same time each year (late September- October) in the same stream section they may encounter each other during spawning and not be genetically isolated. Currently the Department cannot make reliable carcass survey 10

estimates of spring-run upstream of RBDD in the main-stem river because of this overlap between the two runs and the lack of a suitable means of distinguishing them. The difficulties in determining a spring-run estimate on the river include the spring/fallrun mixing and also the occurrence of spring-run from the Feather River Hatchery which commonly stray into the USRB. Using the data from the traditional methodology indicates a mainstem estimate of zero upstream and 30 downstream (Table 1). There is considerable uncertainty and disagreements amongst biologists as to the exact nature of the spring-run population in the main-stem Sacramento River. Until further research is conducted this uncertainty will continue. Similar to winter-run fish, in-river angler harvest of spring-run is considered to be zero due to fishing closures during migration periods and in primary spawning areas, although some poaching and hook mortality associated with trout angling probably occurs. An estimated 168 salmon showing spring-run characteristics passed RBDD in 2005 (Appendix Table A2). This number is less than the 196 spring-run cumulatively counted in Beegum Creek (47), Clear Creek (69) and Battle Creek (80) (Jim Early, USFWS, pers. comm. note: Clear and Battle Creek(s) are draft estimates awaiting results of genetic analysis). Of these fish, only the Beegum Creek salmon were spatially isolated from the fall-run by natural means. A picket weir on Clear Creek was again set-up to isolate the spring-run in the upper reaches of Clear Creek but some spring-run were noted below the weir before it was in place. Five spring-run flights were conducted in late August and September and 105 redds were observed. Sixteen of these were downstream of RBDD before the gates were raised in mid September. Historically the flights in early September were titled Spring-run although it is likely that they are from a mix of fall and spring-run salmon as previously mentioned. In summary, the above RBDD estimate is 196 spring-run salmon. Data for below RBDD includes the tributaries (see below): Antelope (82), Mill (1,150) and Deer Creek(s) (2,239) for a downstream (RBDD to Princeton) spring-run total of 3,501. The total 2005 escapement to the Upper Sacramento River Basin was at least 3,697 (Table 1). Note that Butte (10,625) and Big Chico Creek(s) (37) spring-run results are presented in a separate report (Tracy McReynolds, Department, personal communication). Fall-run Carcass Survey: A fall-run carcass survey was conducted to estimate fall-run spawner populations on the main-stem Sacramento River. An estimated 57,013 salmon spawned in the river from Princeton to Keswick Dam based upon expansion of the fall-run carcass survey data, (Appendix Table A4). The carcass survey was conducted from the Clear Creek Power lines (RM 288.8) upstream to the Keswick Dam in Redding (RM 302) The Jolly-Seber method was used to calculate an estimate of 7,775 natural adult females for this section. This number is expanded to account for redds located outside of the carcass survey reach. Based on aerial redd flight data showing that 69.3% of the main-stem 11

redds were downstream of the carcass area and further expansions for hatchery fish, grilse, and adult males a final estimate of 57,013 for the entire main-stem was developed. Red Bluff Diversion Dam: An estimated 71,159 fall-run salmon passed the RBDD in 2005 (Appendix Table A2). A recurring problem was encountered with the RBDD fallrun estimate in 2005. Results of the hatchery counts for just Battle Creek alone were larger than the total RBDD estimate. For the fifth consecutive year the RBDD estimate resulted in a negative number for the main-stem Sacramento River. The main-stem fallrun RBDD estimate is calculated by using the RBDD total and subtracting the tributaries, harvest, and hatchery estimates (1967-2001). The remaining fish were then assigned to the main-stem and unsurveyed tributaries. It is not known why this large underestimation has occurred for the past five years. A number of possibilities exist including: 1. The fall-run was late arriving to RBDD in 2005. 2. With the temperature control device on Shasta Dam the river water during summer months (when fall-run begin upstream migration) is now colder to ensure winter-run spawning success. The colder water temperature in the river may be allowing fall-run fish arriving in the summer to hold further downstream (beneath RBDD) than was possible before the temperature control began (1998). This may result in reduced fall-run passage at RBDD during the gates-in period of 15 May through 15 September thus impacting the ability to use historical patterns to describe current populations. As a result of these and/or other possibilities it is unlikely that the fall-run data from the RBDD has much value in producing a population estimate. No estimate of angler harvest was made in 2005 due to the lack of funding for the Department s Angler Harvest Project as a result of the State s fiscal crisis. Instead an average harvest percentage for the years 1998-2002 (11.7% of the entire run) was applied to the carcass survey estimate resulting in an estimated 31,903 salmon being taken by anglers, (11,517 above RBDD and 20,386 from RBDD downstream to the Feather River). An estimated 165,259 salmon entered Battle (20,520 in-river and 144,739 CNFH) and Clear creeks (14,824). This number did not include salmon that used other tributaries to the upper main-stem that were not surveyed (Cottonwood, Cow, Paynes, Inks, Bear, and Ash Creek(s) etc.), these systems were traditionally accounted for in the RBDD estimate but this was not the case in 2005 since the main-stem carcass survey is used. Additionally an estimate of 3,372 was made for fall-run escapement (see below) to Mill Creek (2,426) and Deer Creek (946). In summary, total fall-run escapement to the Upper Sacramento River Basin above Princeton is estimated to be at least 272,371 salmon plus an additional number of salmon in unsurveyed areas (Table 1). Appendix Table A5 contains a summary of historical run information from all runs from 1986 to present. Readers should use caution in interpreting these data to meet specific needs. There are numerous categories (total populations, spawner populations, etc) to 12

these data and readers should contact the authors of this report directly to ensure that the data required is available. In most cases the data is available electronically and can be sent directly to interested readers with appropriate categories and data limitations explained. Tributary Specific Estimates Clear Creek Late-Fall-run No escapement estimates were conducted for this run in 2005. Spring-run The U.S. Fish and Wildlife Service (USFWS), Northern Central Valley Fisheries Resource Office (NCVFRO) conducts snorkel surveys in August as an annual index of spring-run Chinook salmon (SRCS) abundance. A total of 69 spring-run was counted in August 2005. A temporary picket weir was installed at Reading bar to spatially separate SRCS from fall-run Chinook salmon (FRCS) spawners. Fall-run Nine weekly FRCS spawner surveys of lower Clear Creek were made during 13 October 2005 through 12 December 2005 in the 6.7 km (4.2 mi) reach downstream of the former McCormick-Saeltzer Dam site. Salmon carcasses were marked by attaching colored tags to the jaw with a hog-ring and placing the fish back into running water for recovery during subsequent surveys. Using fresh carcass mark-and-recovery data with a modified Schaefer model (Hoopaugh, 1978), a spawner population in Clear Creek was estimated to be 14,824 fish (Appendix Table A6). Recapture rates of marked carcasses ranged from 18% to 55%, with a seasonal average of 39%. Based on examination of 5,619 carcasses, the FRCS spawner population in Clear Creek consisted of 33% male adults (fork length [FL] 61 cm [24 in]), 65 % female adults and 2% grilse (FL < 61cm). The seasonal average pre-spawning mortality of female salmon in Clear Creek this season was 1%. A total of 11 coded-wire-tags (CWT s) representing 7 tag codes was recovered during the surveys. All CWT recoveries in Clear Creek were from Coleman National Fish Hatchery (CNFH) releases, (Appendix Table B4). Note: In year 2000 and 2001, approximately 15% of the FRCS hatchery production from all of the Central Valley salmon hatcheries was CWT ed. In 2002 thru 2004, these mass-marked fish were recovered during in-river spawning escapement surveys. Following the pilot mass-marking program, tagging rates for hatchery FRCS returned to low or nonexistent levels; as a result, recovery rates of tagged fish also declined. In 2005 spawning crews encountered relatively few CWT s when compared with returns in 2002 thru 2004. This doesn t mean that fewer hatchery fish are straying into non-natal areas, but rather (due to the low mark rate after 2001), hatchery origin fish aren t identifiable. 13

Cow Creek Late-Fall run No surveys for this run in this tributary were made in 2005. Fall run No surveys for this run in this tributary were made in 2005. Cottonwood Creek Late-fall run No surveys for this run in this tributary were made in 2005. Spring run Forty-seven spring-run Chinook were observed in Beegum Creek a tributary to the Middle Fork of Cottonwood Creek on August 25, 2006. Fall run No surveys for this run in this tributary were made in 2005. Battle Creek Late-fall run No surveys were made for naturally spawning late-fall-run in Battle Creek in 2005. The CNFH reported that 6,435 fish entered the facility. Spring run The USFWS NCVFRO in Red Bluff monitors fish passage in Battle Creek using the CNFH barrier weir. The salmon passing the weir are sampled for genetic analysis and the test results are not final at this time. A draft estimate of 80 SRCS were counted into Battle Creek in 2005. Fall run Eight weekly carcass surveys were made during 20 October and 15 December covering the 5.6 km (3.5 mi) stretch of creek between CNFH barrier weir and the historic CNFH location. Salmon carcasses were marked by attaching colored tags to the jaw with a hog-ring and replacing them back into running water for recovery during following surveys. No surveys were made upstream of the CNFH barrier dam. Gover s ditch, a private irrigation system, was surveyed from the ditch intake to the fish screen. These carcasses are included in the totals for Battle Creek. Using fresh carcass mark-and-recovery data with a modified Schaefer model (Hoopaugh, 1978), total escapement of natural FRCS spawners (including unspawned females) in Battle Creek downstream of CNFH was estimated to be 20,520 salmon (Appendix Table A7). Recapture rates of marked carcasses ranged from 32% to 65% with a seasonal average of 51%. An additional 142,283 salmon entered CNFH. The total 2005 FRCS return to Battle Creek was 162,803. The number of FRCS entering the CNFH in 2005 was the largest in the history of the facility. Both real-time video counts of salmon entering Battle Creek, (Killam, 06-1, 14

2006) and improvements to the mechanical fish processing allowed the hatchery to process this increased number of salmon. This action to allow more fish into CHFH was intended to reduce spawning competition and increase egg survival of fish spawning naturally in Battle Creek. Based on an examination of 10,414 carcasses, the composition of natural spawning FRCS in Battle Creek was 23% male adults (FL 61 cm [24 in]), 75 % female adults and 2% grilse (FL <61cm). Twenty-two percent of the female salmon encountered died before spawning. Female pre-spawning mortality ranged between 4% and 60% for the weekly surveys. FRCS entering CNFH consisted of 44% male adults, 54% female adults and 2 % grilse. A total of 86 potential clipped salmon resulted in 69 CWT s, representing 31 tag codes, were recovered during the surveys. CWT recoveries in Battle Creek were from CNFH and FRH releases, (Appendix Table B4). Antelope Creek Spring run On July 26, 2005 Antelope Creek, Tehama County, was snorkel-surveyed to count holding adult SRCS. Eighty-two adult salmon were observed. A total of 18 miles of stream was surveyed including: the North Fork from 1.5 miles upstream of Judd Creek s confluence to the South Fork confluence, the South Fork from the South Antelope Gun Club to the North Fork confluence, and the main-stem from the North and South Fork confluence to Little Grapevine Creek, (Figure 2 and Appendix Table A8). The areas surveyed encompass the known holding habitat of adult SRCS in Antelope Creek. SRCS habitat Judd Creek Transmission Lines N North Fork Facht Place Antelope Creek South Fork 2 miles Paynes Crossing S.F. Gun Club Figure 2. Antelope Creek, Tehama County. Adult SRCS holding and spawning habitat. 15

In previous years, surveys on the North Fork have started at a boulder cascades upstream of the Judd Creek confluence. Until this year, no salmon had been observed in this area. In 2005, since salmon were observed holding near Judd Creek, surveys were extended upstream for an additional 1.5 miles. Four salmon were observed holding within 300 yards upstream of these boulder cascades. In future surveys, the North Fork snorkel reach will be extended to include these additional holding pools. One SRCS spawning survey was completed on 3 October covering the same survey reaches as the holding survey with the exception that the North Fork upstream of Judd Creek and the main-stem between the canyon mouth and Facht Place was omitted. A total of 22 redds, 4 carcasses and 4 salmon on redds was observed (Appendix Table A8). Water temperature is monitored in Antelope Creek to evaluate stream conditions for holding salmon and to determine potential limitations to salmon survival. Temperature monitors are located at the North and South forks confluence at 1400 feet (ft) elevation and near Paynes Crossing at 1300 ft elevation. During May thru September 2005, average daily water temperatures ranged from 51 Fahrenheit (F) to 68 F (Appendix Figure C1). Survival of adult salmon can be reduced when holding in water temperatures warmer than 59 F. Prolonged exposure of female salmon to water temperatures above 60 F can reduce egg viability, and chronic exposure to water temperatures in excess of 68 F can be lethal to adult salmon (Hinz, 1959). Maximum daily water temperatures equaled or exceeded 68 F during June, July and August at the forks confluence and at Paynes Crossing. Sixty-five percent of the salmon holding in Antelope Creek in 2005 occurred within this 2 mile reach. Given the disparity between the number of salmon counted in July (82) and the number of redds counted in October (22), pre-spawning mortality likely occurred within the summer holding habitat. Mortality could be associated with many factors including thermal stress, secondary infections or predation; but remains unknown at this time. Appendix Table A9 shows the number of days the mean daily water temperature at three monitoring locations in Antelope Creek exceeded tolerances for normal egg viability. In all instances, water temperatures in Antelope Creek, at the locations monitored, were elevated enough to reduce survival. In 2006, additional water temperature monitors are planned in the North and South forks and below Paynes Crossing to investigate the potential of thermal stress limiting adult salmon survival and salmon egg viability in Antelope Creek. This is the first year stream flow was measured for Antelope Creek. Stream flow was calculated by using standard techniques of summing average velocities in a total of 20 channel cross sections. Stream flow at Paynes Crossing on 27 September was 41 cfs. In 2006, flow will be measured weekly during adult salmon migration, holding and spawning periods for the purpose of developing a stage-discharge rating for the mainstem and forks of Antelope Creek during periods when adult SRCS are present. 16

The Department has been monitoring the SRCS population in Antelope Creek, using snorkel observation techniques for the past 17 years (Appendix Table A10). This year s count of 82 is the second highest number of salmon observed in Antelope Creek since snorkel counts began in 1989. During this period, counts have ranged from 0 to 154 salmon. The Department has only limited records of SRCS occurrence in Antelope Creek dating back to the 1950 s. In 1953 and 1956, 127 and 253 SRCS respectively were seined below the Cone Kimball Diversion Dam. (This dam was removed in the 1960 s.) No records exist to show the historical holding or spawning distributions. Fall run No surveys for this run in this tributary were made in 2005. Mill Creek Spring run Between October 4th and 13th, 2005, Mill Creek, Tehama County, was surveyed to count spawning redds of SRCS. Based on these redd counts, an estimated 1,150 SRCS spawned in Mill Creek in 2005. Forty-one miles of spring run spawning habitat was surveyed from upstream of the Highway 36 Bridge crossing downstream to the Steel Tower Transmission Lines (Figure3). Hwy 36 Bridge Mill Creek Camp Spring run habitat Hole-in-the-Ground Sooner Place Rocky Gulch Buckhorn Gulch Avery Place Ranch House Big Bend McCarthy Point Steel Tower Transmission Lines Pape Place Black Rock Blunkall Crossing Sacramento River Little Mill Creek Upper Diversion Dam 5 miles N Figure 3. Mill Creek, Tehama County. Adult SRCS holding and spawning habitat For these surveys, the creek is subdivided into 14 reaches and a team of 2 people walk each reach and enumerate complete redds. In the most remote area of Mill Creek a helicopter is used to enumerate redds from the air. Based on prior years surveys, it is estimated that the peak of spawning activity is Julian weeks 39-41, with spawning 17

starting earlier at higher elevations. In 2005 the upper reaches of spawning were completed during week 40 and the lower reaches were completed during week 41. A total of 184 live salmon, 58 carcasses and 575 redds was observed (Appendix Table A11). In order to expand redd counts to a population estimate, we assume that each female constructs one redd and there is a 1:1 male to female sex ratio in the population. Otherwise stated: each redd represents two salmon: 575 redds x 1 female/redd x 2 = 1150 salmon 1 ( 1 Ratio s of redds to holding SRCS in Deer Creek from 1997-2005 have ranged from 1.1 to 2.5 with a 9-year average of 2.0. For Mill Creek estimates from 1997 thru current, a multiplier of 2 has been used.) Historical migration timing for adult SRCS in Mill Creek was monitored in the late 1950 s (Van Woert, 1964). It was determined that migration reaches a peak during late May and early June. Ninety percent of the fish were counted during the 9-week period: April 29 June 30. By monitoring annual water flow and temperature conditions in Mill Creek during the months of adult SRCS migration, we can determine whether transport conditions were either suitable or limiting for upstream migration of salmon. The maximum water temperature for successful upstream migration of salmon in the Sacramento River system appears to be 65 F (Boles, 1988). Therefore, when average daily water temperatures upstream of water diversion points consistently exceed this 65 F threshold, in can be inferred that upstream migration is over for the season. (Note that this thermal barrier is not influenced by water diversions on the creek since measurements are taken upstream from diversion points). Minimum instream flow to transport adult salmon from the Sacramento River past the first irrigation diversion is not known at this time, although adult FRCS are known to migrate into Mill Creek between 50 and 100 cfs. Appendix Figures C2 and C3 show average daily water flow and temperature both preand post water diversion points in Mill Creek for April thru June. Pre-diversion water temperatures remained below the 65 F threshold until 29 June. Post-diversion flow remained above 135 cfs for the duration of SRCS migration. Post diversion water temperatures remained below the threshold thru 22 June. Based on the above criteria for successful migration, water temperature and flow did not appear to limit the adult SRCS population in Mill Creek in 2005. Water flow and temperature is taken from the Department of Water Resources, Data Exchange Center website: www.cdec.water.ca.gov. This real-time data is provisional and subject to change. Water temperatures monitors in adult salmon holding and spawning areas are used to document the temperature regimes wild salmon holding in. Temperature monitors are located at elevations from 4800 ft down to 1000 ft. Very little information exists on the effects of prolonged elevated water temperatures in maturing Chinook salmon in a stream 18

environment with fluctuating daily temperature regimes. As mentioned previously in Antelope Creek, prolonged temperatures in excess of 60 F may reduce adult and egg survival. Appendix Figure C4 shows the average daily water temperatures within the SRCS holding habitat in Mill Creek. Appendix Table A12 shows the number of days at each elevation that water temperatures exceeded upper tolerance limits for normal egg survival. At all elevations, optimal temperatures for SRCS holding and spawning were exceeded, although elevations between 4200 and 2800 remained below upper tolerance limits for egg survival. Forty-three percent of the salmon spawned in these higher elevations. Twelve percent of salmon spawning occurred above 4200 elevation, and 45% of spawning occurred below 2800. What effect water temperature may have had on egg viability is not known at this time. Also, changes in holding and spawning distributions were not documented in 2005. No spawning took place at elevations below 1400 where temperatures induced mortality may have occurred. Although water flow in the adult SRCS habitat is not measured for Mill Creek, prediversion base flow is measured at the USGS, MLM gage. Base flows ranged between 481 and 100 cfs for the June thru October holding and spawning periods. Redd counts have been used consistently to estimate SRCS escapement since 1997. During this nine-year period, counts have ranged from 202, to 1,594, (Appendix Table A13). Counts of adult SRCS in Mill Creek date back to the late 1940s. An average of 1,900 spring-run Chinook spawned in Mill Creek annually from 1947-1964. Unfortunately, some of these historical datasets include incomplete surveys with unknown expansions and therefore are not comparable to current population data. This years SRCS escapement is comparable to the 2001, 4-year cohort of 1,104 spawners, and is a decrease from the 2002, 3-year cohort of 1,595 spawners. This represents at least average survival during the riverine and ocean phases of a salmon s life cycle and no catastrophic year-class failure. FRCS surveys in Mill Creek are used to determine the extent of temporal and spatial isolation between the two runs. In 2005, FRCS began migrating into Mill Creek on 26 October and spawning peaked the third week in November. SRCS had completed spawning activities prior to the peak of fall-run fish spawning, and therefore remain temporally isolated from FRCS. Five FRCS redds were observed near Little Mill Creeks confluence on 12 December. Also numerous FRCS were observed ascending the upper diversion dam this year; these observations confirm that salmon ascended to at least 1000ft. No time or personnel were available to determine the upstream limits of FRCS spawning. Although no SRCS redds were observed below 1400 elevation, it is not known whether spatial isolation was maintained between the two runs in 2005. Fall run Four weekly spawner surveys were made between 11 November and 8 December covering a 5 mile reach between the Los Molinos Mutual s Upper Diversion Dam and the confluence with the Sacramento River. Salmon carcasses were marked by attaching colored tags to the jaw with a hog ring and replacing the carcass back into running water for recovery during subsequent surveys. 19

Using fresh carcass mark-and-recovery data with a modified Schaefer model (Hoopaugh, 1978), the minimum FRCS spawner escapement into Mill Creek was estimated to be 2,246 salmon (Appendix Table A8). Recapture rates of marked carcasses ranged from 30% to 58% and averaged 48%. Due to personnel shortages, surveys were not conducted upstream of the Upper Diversion Dam. Anecdotally, numerous FRCS were observed ascending the fish ladder at Upper Dam, and, as noted previously, ascended to at least 1000 ft elevation. Since only a portion of the spawning habitat was surveyed in 2005, the reported FRCS escapement into Mill Creek in 2005 represents a minimum value. The composition of natural spawning FRCS in Mill Creek was 44% male adults (FL 61 cm [24 in], 54 % female adults and 3 % grilse (FL < 61 cm), based on an examination of 1,085 carcasses. Only 0.3 % of the female carcasses encountered were pre-spawned mortalities. Three CWT s from 4 salmon (representing 3 tag codes) were recovered during the carcass surveys. All CWT recoveries were from CNFH releases, (Appendix Table B4). If water temperatures during egg incubation and fry development exceed 57.5 F, abnormally high egg and fry loss can occur, (Healey, 1977). Due to water temperature concerns, the Department requested that Los Molinos Mutual Water Company (LMMWC) delay bypassing fall flows until the average daily water temperature dropped below this 57.5 F threshold. (In previous years, bypass flows at temperatures above critical levels have resulted in pre-spawning mortality of adult salmon.) LMMWC agreed to incrementally release water so we could determine minimum flows to transport adult salmon over critically shallow riffles. Coincident with these metered flows, a storm event increased base flow from 33 to 91 cfs between 26 October and 27 October (Appendix Figure C5). Consequently, salmon were instantly attracted into Mill Creek and minimum fish transport flows could not be determined. This effort will be repeated in 2006. Deer Creek Spring run On 9 August, 2005, Deer Creek, Tehama County, was snorkel surveyed to count holding adult SRCS. A total of 2,239 SRCS was observed (Appendix Table A15). Twenty-four miles of stream was surveyed from the Upper Deer Creek Falls downstream to within 2 miles of Dillon Cove (Figure 4). This encompasses the known holding habitat of adult SRCS in Deer Creek. 20

Potato Patch SRCS habitat Wilson Cove Lower Falls Upper Falls Red Bridge A-Line N Polk Springs Murphy Trail Trail 2E17 17 miles to Sacramento River Ponderosa Way Powerlines Dillon Cove 5 miles Figure 4. Deer Creek, Tehama County, adult SRCS habitat. SRCS spawning surveys were completed between 28 September and 13 October using a combination of aerial and ground surveys to count redds, fish on redds and carcasses. Lassen National Forest fisheries crews completed the ground surveys between the Upper Deer Creek Falls and Ponderosa Way. (The vegetation in this area is too dense for effective aerial redd counts.) A helicopter was used to count redds between Ponderosa Way and the Steel Tower Transmission Lines. A total of 1,271 redds, 196 carcasses and 220 fish on redds were observed on all surveys (Appendix Table A14.) Both the adult holding survey and the spawning survey remain one pass surveys. The holding counts serve as an index of abundance and document relative holding and spawning distribution within the watershed. This minimalist survey strategy reduces stress on holding salmon, and allows for the continuation of annual surveys thru ever increasing cuts to budgets and personnel. Actual timing and duration of adult SRCS migration into Deer Creek is not known. Although, by monitoring water flow and temperature conditions in Deer Creek during the spring months, we can infer whether transport conditions limited upstream migration of adult salmon. As previously mentioned in Mill Creek, when average daily water temperatures upstream of water diversion points consistently exceed the 65 F temperature threshold, it can be inferred that upstream migration is over for the season. Minimum instream flow to transport adult salmon from the Sacramento River past the first irrigation diversion is not known at this time, although adult FRCS are known to migrate into Deer Creek between 50 and 100 cfs. Appendix Figure C6 shows average daily water temperature and flows both pre- and post water diversion points in Deer Creek for April thru June. Pre-diversion water temperature remained consistently above 65 F after 22 June. Post-diversion water 21

temperature remained consistently above the threshold after 21 June. Flows for fish migration remained greater than 100 cfs thru 21 June. Based on the above criteria, water temperature and flow did not appear to limit adult SRCS migration into Deer Creek in 2005. Water temperatures in adult salmon holding and spawning habitat of Deer Creek are monitored to document the temperature regimes wild self-sustaining stocks of salmon are surviving in Appendix Table A16 and Appendix Figure C7 show the number of days at each elevation that water temperatures exceeded tolerance limits for normal egg survival. In all the holding areas, some temperature exceedence occurred. At elevations > 2000 ft, temperatures were below mortality levels. In 2005, 87% of SRCS in Deer Creek were holding at elevations >2000ft. It s important to remember that Deer Creek is an unregulated stream. The temperature regimes these salmon are subjected to cannot be altered and likely have not changed from historical times. The last remaining streams capable of supporting SRCS in California s Central Valley contain only marginal habitat when compared to historical holding and spawning areas. Whether water temperature is a limiting factor in the few streams still supporting viable populations of SRCS is not known at this time. Although water flow in the adult SRCS holding habitat is not measured in Deer Creek, pre-diversion base flow is measured at the USGS, DVD gage. Base flows ranged between 68 and 380 cfs for the June thru October holding and spawning periods. During the previous 14 years SRCS counts in Deer Creek have ranged from 209 to 2,759 salmon (Appendix Table A17). This year s count of 2,239 is the second highest on record since snorkel counts have consistently been used to monitor Deer Creeks salmon population. Between 1940 and 1964, an average of 2,200 SRCS was counted annually using fish ladder counts and carcass surveys. Unfortunately, these historical surveys were often expansions of partial weir counts and incomplete surveys and therefore not comparable to current survey results. This year s count represents an increase of both the 2001 and 2002 three- and four-yearold cohorts of 2,186 and 1,622 salmon respectively. Although this increase cannot be attributed to any one activity, it suggests better than average survival during the riverine and ocean phases of a salmons life cycle. (The annual age structure of salmon returning to Deer Creek is not known since too few carcasses are encountered to determine ratios of returning year classes.) Fall run Weekly FRCS spawning surveys were made between 12 November and 15 December between the USGS gage upstream of Deer Creek Irrigation District s upper diversion dam and the Highway 99 bridge crossing. (A small percentage of salmon may have spawned upstream of the survey reach.) Fresh salmon carcasses were marked by attaching colored tags to the jaw with a hog ring and replacing the carcass back into running water for recovery on subsequent surveys. A total of 455 carcasses and 527 redds were counted during these surveys. 22

Due to the limited number of carcasses encountered, a seasonal mark and recapture rate was used to estimate the spawning population. Using Chapman s version of the Peterson equation (Ricker 1975), the FRCS spawner population in Deer Creek was estimated to be at least 946 fish (Appendix Table A18). The seasonal recapture rate of marked carcasses was 46%. Based on an examination of 416 carcasses, composition of natural spawning FRCS in Deer Creek was 46% male adults (FL 61 cm [24in]), 51% female adults and 2% grilse (FL, 61cm [24in]). Less than 1% of the female carcasses examined were unspawned. One of the carcasses encountered was adipose fin clipped for a CWT. No CWT was recovered from this fish (Appendix B). Since only a small fraction of each hatcheries production receives a CWT, a large percentage of FRCS returning to tributaries of the Sacramento River may be strays from one of the five salmon hatcheries in California s Central Valley. No surveys were made to verify when FRCS first entered Deer Creek, although it is doubtful that combined flow and temperature conditions were favorable for successful FRCS migration prior to 26 October. Appendix Figure C8 shows the average daily water temperature and flow in Deer Creek during the October thru December 2005 FRCS spawning period. Pre-diversion water temperatures dropped below the 57.5 degree spawning threshold after 15 October, and post-diversion temperatures dropped below this threshold after 26 October. Although minimum flows necessary for unimpeded migration in Deer Creek have not been established, an October 26th and 28 th rain event increased the fish attraction flow in lower Deer Creek to over 50 cfs., which may have attracted FRCS into Deer Creek. Pre-diversion flow increased to 110 cfs. Surveys to determine FRCS escapement into Deer Creek have occurred sporadically since 1952. These estimates have ranged from 12,000 to 10 fish. Many of these surveys were one-time passes and carcass expansion techniques were poorly documented. Therefore, long-term population trends cannot be inferred from the existing data. ACKNOWLEDGEMENTS The authors wish to thank everyone who assisted us with the collection of the information and administration of activities in this report. Many individuals participated in the data collection efforts associated with the escapement estimates listed in this report. Individual thanks are given to the following: From the Department: Randy Benthin, Alice Low, Brett Rohrer, Steve Arrison, Steve Baumgartner, Mike Berry, Larry Hanson, Mike Dean, Terri Moore, Andy Holland, Matt Johnson, Ed Martin, Ira Alexander, Amber Leininger, Audrey Silbernagel and Mara Kraemer, Rich Anthes, Shannon Stewart, Becky Mitchell, Paula Lohmeyer, Allen Grover, David Grant, Stacey Standish, Jim Chakarun, Tony Welsh, Devon Rohrer, Curt Babcock, and James Lyons. From the USFWS: Jim Smith, Kevin Niemala, Matt Brown, Sarah Giovannetti, Shea Gaither, Joe Chigbrow, 23

Andrew Hill, Jonathan Thompson, Angela Webb Jim Early, Naseem Alston, Bob Null, Kevin Offill, Bill McKinney, Mike Ricketts, Josh Gruber, Laura Mahoney, Curtis Brownfield, Rob Emge, Scott Hammelberg, Sharon Grover, Paula Wittner, Vicky Van Gundy, and Debbie Anderson. From the National Marine Fisheries Service: Howard Brown and Daniel Burch. From Lassen National Forest: Ken Roby, Ryan Foote, Melanie McFarland, Flori Consalati, Susie Elkjer, Bobette Jones, Elise LaVanaway, Chris Mayes, Jennifer Robinson, Kurt Sable, Rebecca Degagne, Jason Gritzner, and Karl Anderson. From Lassen National Park: Nancy Nordstein. From Sierra Pacific Industries: Julie Kelley. From Metropolitan Water District: Bridgett Adams. Additionally we thank the Mill and Deer Creek Conservancies, and landowners Judd Hanna and Keri Burke and the many individual land owners who allow access to their properties for stream surveys. We would also like to thank the staffs and organizations who assisted us in completion of the work described in this report. These include: Redding Air Services, Sierra Pacific Industries, U.S. Forest Service, NOAA Fisheries, U.S. Bureau of Reclamation, and the Department of Water Resources. 24

REFERENCES Boles, G. L., S.M. Turek, C. C. Maxwell, and D. M. McGill. 1988. Water temperature effects on Chinook salmon (Oncorhynchus tshawytscha) with emphasis on the Sacramento River: a literature review. Calif. Dept. Water Res. 44pp. California Department of Fish and Game. 1998. A status review of the spring-run Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento River drainage, Candidate Species Status Report 98-01, June 1998. Healey, T.P., 1979. The effect of high temperature on the survival of Sacramento River Chinook (King) salmon, Oncorhynchus tshawytscha, eggs and fry. Cal. Dept. Fish and Game, Anad. Fish Admin. Rept. 79-10. Hinz, J.A. 1959 in CDFG, 1998. Annual Report: Nimbus salmon and steelhead hatchery, fiscal year, 1957-1958. Cal. Dept. Fish and Game, Inld. Fish. Div. Admin. Rept. 59-4. Hoopaugh, David. A. (ed.). 1978. King (Chinook) salmon spawning stocks in California s Central Valley, 1976. Calif. Dept of Fish and Game, Anad. Fish. Br. Admin. Rep. No. 78-19. 33p. National Marine Fisheries Service. 1996. Recommendations for the recovery of the Sacramento River winter-run Chinook salmon. Nat. Marine Fish. Serv. Southwest Region. Long Beach, CA 228 p. Killam, D. S. 2006. Sacramento River Winter-run Chinook Salmon Escapement Survey April-September 2005. SRSSAP Tech. Report No. 06-2, 2005. 35p Killam, D.S. 2006. Results of an Experimental Video Station for Fall-Run Chinook Salmon escapement into Battle Creek for years 2003-2005. SRSSAP. Tech. Report No. 06-1, 2006. (in preparation). Ricker, W.E. 1975. Computation and Interpretation of Biological Statistics of Fish Populations. Res. Bd. Canada, Bull. 91. 382 p. Schaefer, M.D. 1951. Estimation of size of animal populations by marking experiments. U.S. Fish and Wildl. Serv., Fish Bull. 52: 189-203. Van Woert, W. 1964. Mill Creek counting station. Office memorandum to Eldon Hughes, May 24, 1964. Calif. Dept. Fish and Game, Water Projects Branch, Contract Services Section, 7pp. 25

APPENDIX A (Data Tables) Appendix Table A1. Average migration timing for the various salmonid runs passing the Red Bluff Diversion Dam 1970-1988. 26

Appendix Table A2. Summary of 2005 Red Bluff Diversion Dam fish passage information. Readers note: to better access this and following data tables use the zoom function of your software. 27

Appendix Table A3. Summary of aerial redd counts for Sacramento River System from Keswick Dam downstream to Princeton Ferry from 1969-2005. Percentages of redds in main-stem Sacramento from aerial flights (up and downstream of RBDD) YEAR Winter-Run Spring-Run Fall-Run Late-Fall ALL COMBINED % Up % Down % Up % Down % Up % Down % Up % Down % Up % Down 1969 n/a n/a n/a n/a 74.4% 25.6% n/a n/a 74.4% 25.6% 1970 n/a n/a n/a n/a 85.6% 14.4% n/a n/a 85.6% 14.4% 1971 n/a n/a n/a n/a 68.5% 31.5% n/a n/a 68.5% 31.5% 1972 n/a n/a n/a n/a 63.5% 36.5% 67.2% 32.8% 64.8% 35.2% 1973 n/a n/a n/a n/a 69.9% 30.1% 75.9% 24.1% 74.7% 25.3% 1974 n/a n/a n/a n/a 60.9% 39.1% n/a n/a 60.9% 39.1% 1975 n/a n/a n/a n/a 56.4% 43.6% n/a n/a 56.4% 43.6% 1976 n/a n/a n/a n/a 72.9% 27.1% 64.7% 35.3% 71.9% 28.1% 1977 n/a n/a n/a n/a 45.1% 54.9% n/a n/a 45.1% 54.9% 1978 n/a n/a n/a n/a 46.0% 54.0% 25.6% 74.4% 43.2% 56.8% 1979 n/a n/a n/a n/a 53.9% 46.1% 42.7% 57.3% 52.0% 48.0% 1980 n/a n/a n/a n/a 48.7% 51.3% n/a n/a 48.7% 51.3% 1981 87.8% 12.2% n/a n/a 63.0% 37.0% 63.5% 36.5% 63.5% 36.5% 1982 97.0% 3.0% n/a n/a 67.1% 32.9% n/a n/a 67.5% 32.5% 1983 n/a n/a 81.1% 18.9% 47.6% 52.4% 71.2% 28.8% 59.3% 40.7% 1984 n/a n/a 93.3% 6.7% 66.6% 33.4% 78.9% 21.1% 67.2% 32.8% 1985 71.8% 28.2% 78.6% 21.4% 55.5% 44.5% 81.5% 18.5% 56.3% 43.7% 1986 n/a n/a 100.0% 0.0% 64.5% 35.5% 72.8% 27.2% 64.9% 35.1% 1987 95.5% 4.5% n/a n/a 71.4% 28.6% 64.1% 35.9% 71.0% 29.0% 1988 74.5% 25.5% 97.4% 2.6% 77.9% 22.1% 98.9% 1.1% 78.3% 21.7% 1989 97.9% 2.1% 100.0% 0.0% 83.3% 16.7% 41.9% 56.4% 82.6% 17.4% 1990 93.3% 6.7% 100.0% 0.0% 66.8% 33.2% 87.4% 12.6% 67.8% 32.2% 1991 100.0% 0.0% 100.0% 0.0% 66.9% 33.1% 81.6% 18.4% 67.8% 32.2% 1992 96.4% 3.6% 100.0% 0.0% 73.8% 26.2% 85.8% 14.2% 75.1% 24.9% 1993 97.7% 2.3% 100.0% 0.0% 72.5% 27.5% 100.0% 0.0% 72.7% 27.3% 1994 100.0% 0.0% 85.1% 14.9% 77.8% 22.2% 77.0% 23.0% 77.8% 22.2% 1995 99.4% 0.6% 90.9% 9.1% 83.5% 16.5% 61.9% 38.1% 83.5% 16.5% 1996 100.0% 0.0% 100.0% 0.0% 85.5% 14.5% n/a n/a 86.0% 14.0% 1997 100.0% 0.0% 99.0% 1.0% 82.8% 17.2% n/a n/a 83.6% 16.4% 1998 97.5% 2.5% 100.0% 0.0% 90.5% 9.5% 97.2% 2.8% 92.4% 7.6% 1999 100.0% 0.0% 100.0% 0.0% 78.8% 21.2% n/a n/a 99.0% 1.0% 2000 100.0% 0.0% 100.0% 0.0% 90.8% 9.2% 98.6% 1.4% 94.7% 5.3% 2001 99.6% 0.4% 96.6% 3.4% 85.4% 14.6% 95.2% 4.8% 93.1% 6.9% 2002 99.8% 0.2% 100.0% 0.0% 69.3% 30.7% 100.0% 0.0% 80.5% 19.5% 2003 99.7% 0.3% 100.0% 0.0% 74.5% 25.5% 97.3% 2.7% 79.8% 20.2% 2004 100.0% 0.0% 100.0% 0.0% 78.1% 21.9% 100.0% 0.0% 87.1% 12.9% 2005 100.0% 0.0% 84.8% 15.2% 78.8% 21.2% 90.2% 9.8% 90.9% 9.1% AVERAGE 95.8% 4.2% 95.8% 4.2% 70.2% 29.8% 77.7% 22.2% 72.7% 27.3% n/a = not available 28

Appendix Table A4. Summary of the 2005 carcass survey results for the main-stem Sacramento River salmon populations. 2005 Mainstem Sacramento River Late-fall-run Chinook Salmon TOTAL POPULATION ESTIMATE ESTIMATE Adjustments Template Calculation for Female Adults 2,108 2,108 From the Jolly-Seber mark-recapture formulas Adult Female Ad-Clipped Fish In-River Adjustment 2,426 1.1506 * Based on Adult Female Fresh Carcasses with Ad-clips (47) of 359 total / 312 natural. Number of All Adult Females-Downstream Redd Factor 4,657 1.9196 103 of 215 total redds below carcass survey location assume adult fish. Number of All Adult Males Adjustment Factor 4,250 0.9126 ^ Based on the ratio of male adults to female adults at CNFH: (2517 male to 2758 female or 47.7% to 52.3%) Number of All Female Grilse Adjustment Factor 26 0.0056 Based on the female grilse (<610mm) to female adults from carcass survey fresh fish sample ( 361 total: 2 jills to 359 adults) Number of All Male Grilse Adjustment Factor 1,591 0.3744 Based on the male grilse (<610mm) to male adults from the carcass survey fresh fish sample ( 268 total: 73 jacks to 195 adults). Number of Fish Removed from Population by LSNFH 77 77 USFWS Data from Keswick Collections 2005. Includes sacrificed and transferred not winter fish Final Estimate is 10,601 = 10,601 This number includes only Late-fall salmon in the Sacramento River Mainstem Survey conducted from 14 Dec 2004 through 6 May 2005. Total of 22 Survey Periods:Large female Tally = Tagged 590, Chopped 604 Examined 1473, Recaptured 279. Recapture rate of 47.3% 2005 Mainstem Sacramento River Winter-run Chinook Salmon TOTAL POPULATION ESTIMATE ESTIMATE Adjustments Jolly-Seber Model Calculation for Large Females 7,205 7,205 From the Jolly-Seber mark-recapture formulas Large Female Ad-Clipped Fish Adjustment 8,999 1.2490 3005 large females were seen / 2406 were not ad-clipped Number Large Females: Downstream Redds Factor 8,999 1.0000 1968 redds were seen / 1968 were in the survey area Adult Females estimated: 9,005, Jills: 42 Number Large Males from Keswick Trap Data 5,759 0.6400 144 Large Males / 225 Large Females at Keswick Trap Adult Males estimated: 5,573, Jacks: 1,110 Total In-River Females (including jills) 9,047 1.0053 Based on Total / Large (3021/3005) Females in carcass data Total In-River Males (including jacks) 6,683 1.1604 Based on Total / Large (1042/898) Males in carcass data Fish Removed from In-River by LSNFH 109 109 Number of Salmon taken into LSNFH Hatchery Final Estimate is 15,839 Survey conducted from 28 April through 2 Sep 2005. Total of 43 Survey Periods:Large female Tally = Tagged 3,476, Chopped 1,787 Examined 7,581, Recaptured 2,318. Recapture rate of 66.7% 2005 Mainstem Sacramento River Fall-run Chinok Salmon TOTAL POPULATION ESTIMATE ESTIMATE Adjustments Template Calculation for Female Adults (From Below) 7,775 7,775 From the Jolly-Seber mark-recapture formulas Adult Female Ad-Clipped Fish In-River Adjustment 7,915 1.0179 Based on Adult Female Fresh Carcasses with Ad-clips (16 of 909), (1.8% clipped vs 98.2% natural.) Number of All Adult Females-Downstream Redd Factor 25,744 3.2527 (A total of 1210 redds were observed during FR surveys -372 were within carcass survey boundaries: 30.7%) Number of All Adult Males Adjustment Factor 29,000 1.1265 Based on the ratio of male adults to female adults at RBDD Trap: (481-male to 427-female or 53.0% to 47.0%) Number of All Female Grilse Adjustment Factor 170 0.0066 Based on the female grilse (<610mm) to female adults from carcass survey fresh fish sample (6 jills to 909 adults or 0.7% to 99.3%). Number of All Male Grilse Adjustment Factor 2,099 0.0724 Based on the male grilse (<610mm) to male adults from the carcass survey fresh fish ( 27 jacks to 373 adults or 6.75% to 93.25%). Final Estimate is 57,013 = 57,013 Survey conducted from 20 Sep 2005 through 29 Dec 2005. Total of 14 Survey Periods: Adult FemalesTagged 1,957, Chopped 2,240, Examined 4,954, Recaptured 757. Recapture rate of 39% 29

Appendix Table A5. Summary of the Chinook salmon population estimates by run in the Upper Sacramento River Basin, upstream of Princeton (RM 164) for the years 1986-2005. YEAR ** Salmon Totals for Sacramento System above Princeton ^ Fall Spring Winter Late-Fall TOTALS 1986 144,377 17,657 2,596 11,398 176,029 1987 134,686 11,435 2,186 26,438 174,746 1988 159,448 11,003 2,886 12,937 186,273 1989 96,271 5,895 696 31,261 134,123 1990 71,799 5,305 430 8,150 85,683 1991 56,277 1,607 211 8,591 66,686 1992 51,588 876 1,240 11,944 65,649 1993 71,314 716 387 n/a 72,416 1994 112,923 2,221 186 n/a 115,330 1995 169,556 2,082 1,297 n/a 172,935 1996 172,058 1,520 1,337 n/a 174,915 1997 249,118 793 880 n/a 250,791 1998 119,114 4,096 3,002 46,454* 172,666 1999 308,745 2,660 3,288 32,368* 347,061 2000 184,987 1,442 1,352 16,015* 203,796 2001 232,601* 3,715 5,523 / 8,100* 25,725* 270,141 2002 571,169* 4,445 9,172 / 7,441* 40,101* 623,156 2003 287,876* 4,423 9,757 / 8,218* 9,485* 310,002 2004 162,596* 2,380 7192 / 7,869* 16,663* 189,426 2005 272,370* 3,697 5,299 / 15,839* 19,776* 311,683 AVERAGE 181,444 4,398 3,472 21,154 152,866 ^ Data from RBDD counts + aerial redd flights + tributary surveys beneath RBDD ** Totals reflect available data, many streams not surveyed have populations of salmon * These estimates calculated using carcass survey results, hatchery, angler and redd surveys Note: Winter run average is calculated using RBDD numbers from 1986 till 2000 and carcass numbers after 2000 30

Appendix Table A6. Chinook salmon carcass mark-and-recovery data used to estimate the 2005 fall-run spawner population in Clear Creek from the former McCormick-Saeltzer Dam site to 6.4 km downstream, using the modified Schaefer equation. Total Recovery Marked Total Period (j): Carcasses Carcasses Population Number of marked carcasses recovered from marking period (i): recovered observed estimate 1 2 3 4 5 6 7 8 (Rj) (Cj) 1 (N) 2 17 Oct 5 5 271 2,011 24 Oct 4 25 29 712 1,385 31 Oct 1 6 50 57 835 2,798 7 Nov 14 29 43 704 2,730 14 Nov 1 7 31 38 77 1,411 1,634 21 Nov 2 5 17 65 89 1,125 2,000 2 Dec 2 4 15 31 52 635 1,560 12 Dec 3 10 11 24 302 707 Recovery R(i) 11 31 73 67 59 83 41 11 Marked M(i) 55 64 196 172 107 173 138 61 Total Estimate: 14,824 1 Includes salmon carcasses which were marked and marked carcasses that were recovered. 2 Adjusted estimate reflects the modified Schaefer equation (Hoopaugh 978), where marked carcasses (Mi) from the second marking period on were subtracted from the total estimate. Appendix Table A7. Chinook salmon mark-and-recovery data used to estimate the 2005 fall-run spawner population in Battle Creek from Coleman NFH to the old hatchery site. Carcass data includes unspawned females. Total Recovery Marked Total Period (j): Carcasses Carcasses Population Number of marked carcasses recovered from marking period (i): recovered observed estimate 1 2 3 4 5 6 7 8 (Rj) (Cj) 1 (N) 2 28 Oct 93 93 2,157 3,702 3 Nov 11 128 139 2,131 3,946 10 Nov 3 7 54 64 1,325 4,866 17 Nov 2 7 28 108 145 1,962 2,415 23 Nov 1 5 23 185 214 1,915 2,350 5 Dec 2 8 13 65 88 1,185 2,620 15 Dec 1 1 7 55 64 390 621 Recovery R(i) 110 142 60 140 198 72 55 Marked M(i) 168 272 295 206 285 223 122 Total Estimate: 20,520 1 Includes salmon carcasses which were marked and marked carcasses that were recovered. 2 Adjusted estimate reflects the modified Schaefer equation (Hoopaugh 978), where marked carcasses (Mi) from the second marking period on were subtracted from the total estimate. Appendix Table A8. Holding and spawning distribution of adult SRCS in Antelope Creek, 2005. Holding Survey Spawning Survey Section # of salmon % of total # of redds % of total North Fork 18 22 0 0 South Fork 0 0 6 27 Main stem to Paynes 53 65 12 55 Paynes to canyon mouth 10 12 4 18 Canyon mouth to Power Lines 1 1 ns -- Power Lines to Facht Place 0 0 ns -- Totals 82 100% 22 100% 31

Appendix Table A9. Water Temperature Exceedence in Antelope Creek SRCS habitat, 2005. Exceeding Location Elevation Period of Record 59.0 F normal egg viability North Fork @ Judd Ck N and S Fork confluence Number of Days Mean Daily Temperature 63.5 F reduced egg viability 68.0 F partial mortality 1900 ft 6/18/05 to 10/31/05 58 9 0 1400 ft 5/1/05 to 10/31/05 69 41 1 Paynes Crossing 1300 ft 5/1/05 to 8/1/05 45+ 34+ 17+ Appendix Table A10. Summary of SRCS counts in Antelope Creek by reach: 1983-2005. Section North Fork 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 Judd Creek to South Fork 0 ns ns ns ns ns 0 0 0 9 5 0 1 0 6 0 18 South Fork S.A. Gun Club to North Fork ns ns ns ns ns ns 1 0 0 9 0 1 1 0 0 0 0 Main Stem Confluence to Paynes 2 1 0 0 3 0 2 0 0 77 19 2 4 31 29 3 53 Paynes to Canyon Mouth 0 ns ns ns 0 ns 4 1 0 23 6 1 1 1 7 0 10 Canyon Mouth to Power Lines ns ns ns ns ns ns ns ns ns 25 5 4 1 8 4 0 1 Power Lines to Facht Place ns ns ns ns ns ns ns ns ns 11 2 1 0 6 0 0 0 Totals 2 1 0 0 3 0 7 1 0 154 40 9 8 46 46 3 82 Appendix Table A11. Spawning distribution of adult SRCS in Mill Creek, 2005. Survey Reach # of Redds Counted % of Total Above Hwy 36 7 1 Hwy 36 to Little Hole-in-Ground 10 2 Little Hole-in-Ground to Hole-in-Ground 49 9 Hole-in-Ground to Ishi Trailhead 47 8 Ishi Trailhead to Big Bend 19 3 Big Bend to Canyon Camp 51 9 Sooner Place to McCarthy 70 12 McCarthy to Savercool 61 11 Savercool to Black Rock 46 8 Black Rock to Ranch House 79 14 Ranch House to Avery 78 13 Avery to Pape 36 6 Pape to Buckhorn 22 4 Buckhorn to Transmission Lines 1 0 0 Total Redds 575 100% Population Estimate (redds x 2) 1150 1 Helicopter Survey 32

Appendix Table A12. Water temperature exceedence in Mill Creek adult SRCS habitat, 2005. Number of Days Equal or Exceeding normal reduced partial survival survival mortality # of daily 59 F 63.5 F 68 F Location Elevation records Hwy 36 4800 142 78 34 0 Hole-Ground 4200 142 50 1 0 Sooners 2800 184 17 0 0 Black Rock 2100 184 77 43 1 Rancheria 1600 90 17 4 0 Little Mill 1000 184 96 69 33 Appendix Table A13. Summary of SRCS redd counts and population estimates in Mill Creek, 1997-2005. Section 1997 1998 1999 2000 2001 2002 2003 2004 2005 Above Hwy-36 0 NS 1/ NS NS NS 12 0 0 7 Hwy-36 to Little Hole-in-the-Ground 1 1 0 0 3 13 6 1 10 Little Hole-in-the-Ground to Hole-in-the-Ground 7 2 1 0 19 23 14 23 49 Hole-in-the-Ground to Ishi Trailhead 1 1 3 4 13 38 44 5 47 Ishi Trailhead to Big Bend 7 1 11 6 14 8 24 9 19 Big Bend to Canyon Camp 53 11 6 12 92 103 121 49 51 Canyon Camp to Sooner Place Not surveyed Sooner Place to McCarthy 19 21 22 59 129 172 133 97 70 McCarthy to Black Rock 1 25 75 77 153 119 137 95 107 Black Rock to Ranch House 5 19 58 34 71 127 39 38 79 Ranch House to Avery Place 7 33 53 44 2/ 83 67 146 78 Avery Place to Pape Place NS 39 }52 15 12 2/ 27 2/ 58 8 36 Pape Place to Buckhorn Gulch NS 13 12 2/ 3 2/ 0 2/ 63 2/ 64 18 22 Buckhorn Gulch to Blunkall Crossing NS 25 23 2/ 9 2/ 0 2/ 0 3 2/ 0 2/ Blunkall Crossing to Little Mill Creek NS 17 17 2/ 0 2/ 0 2/ 0 3 2/ 10 2/ 0 2/ Little Mill Creek to Transmission Line NS 4 0 2/ 0 2/ 0 2/ 9 2/ 0 0 2/ Total Redds 101 212 280 272 552 797 713 499 575 Population Estimate 202 424 560 544 1,104 1,594 1,426 998 1,150 1/ NS = not surveyed 2/ Estimated redds from a ground: aerial redd survey ratio. 33

Appendix Table A14. Chinook salmon mark-and-recovery data used to estimate the 2005 fall-run spawner population in Mill Creek from the Los Molinos Mutual Upper Diversion Dam downstream to the confluence with the Sacramento River, using the modified Schaefer equation. Total Recovery Marked Total Period (j): Carcasses Carcasses Population Number of marked carcasses recovered from marking period (i): recovered observed estimate 1 2 3 (Rj) (Cj) 1 (N) 2 18 Nov 24 24 400 733 28 Nov 4 52 56 384 860 8 Dec 13 20 33 443 832 Recovery R(i) 28 65 20 Marked M(i) 48 120 67 Total Estimate: 2,426 1 Includes salmon carcasses which were marked and marked carcasses that were recovered. 2 Adjusted estimate reflects the modified Schaefer equation (Hoopaugh 1978), where marked carcasses (Mi) from the second marking period on were subtracted from the total estimate. Appendix Table A15. Holding and spawning distribution of adult SRCS in Deer Creek, 2005. Section Holding Survey Spawning Survey # of salmon % of total # of redds % of total Upper Falls to Potato Patch 204 9 163 13 Potato Patch to Hwy32 Bridge 96 4 92 7 Hwy32 Bridge to Lower Falls 46 2 9 1 Lower Falls to A-Line 422 19 161 13 A-Line to Wilson Cove 300 13 428 33 Wilson Cove to Polk Springs 466 21 114 9 Polk Springs to Murphy Trail 423 19 169 13 Murphy Trail to Ponderosa Way 238 11 135 11 Ponderosa Way to Trail 2E17 40 2 8 <1 Trail 2E17 to Dillon Cove 4 <1 2 <1 Dillon Cove to Transmission Lines No survey 0 0 Totals 2,239 100% 1,281 100% Appendix Table A16. Water temperature exceedence in Deer Creek SRCS habitat, 2005. Number of Days Equal or Exceeding # of daily Normal survival Reduced Survival Partial mortality Location Elevation records 59 F 63.5 68 F Upper Falls 3600 ft 142 6 0 0 Lower Falls 3000 ft 145 47 3 0 Wilson Cove 2700 ft 184 58 18 0 Murphy Trail 2000 ft 138 62 31 1 Trail 2E17 1500 ft 184 88 59 26 34

Appendix Table A17. Summary of SRCS holding and spawning distribution and population counts in Deer Creek, 1992-2005 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 Section Elev. hold hold hold hold hold hold spawn hold spawn hold spawn hold spawn hold spawn hold spawn hold spawn hold spawn hold spawn Upper Falls to Potato Patch 3600 12 35 100 267 67 102 63 14 1 114 126 34 26 204 80 311 128 283 135 114 36 204 163 Potato Patch to Hwy 32 5 17 31 67 44 19 30 11 5 91 100 45 19 131 70 78 90 198 56 19 11 96 92 Hwy 32 to Lower Falls 7 4 4 37 12 9 14 4 27 28 72 7 13 59 24 52 35 35 25 4 46 9 98 Lower Falls to A-Line 3000 65 54 215 225 170 153 94 93 38 241 95 151 34 357 140 492 217 389 163 151 422 161 A-Line to Wilson Cove 2700 13 35 2 134 67 22 7 98 31 167 396 76 48 149 104 160 57 405 189 75 48 300 428 Wilson Cove to Polk Springs 51 4 69 124 88 26 1 182 35 158 188 96 43 346 45 451 167 647 195 141 71 466 114 Polk Springs to Murphy Trail 2000 21 51 56 219 102 59 26 270 59 247 150 92 36 303 107 350 82 393 154 178 33 423 169 Murphy Trail to Ponderosa Way 1700 35 59 8 177 58 74 40 615 373 355 167 135 37 34 132 183 174 320 141 112 96 238 135 Ponderosa Way to Trail 2E17 1500 ns ns ns 45 8 2 0 476 119 106 100 1 ns 37 2 107 77 29 10 1 40 8 Trail 2E17 to Dillon Cove ns ns ns ns ns ns ns 116 105 50 103 0 ns 2 11 1 72 12 ns ns ns 4 2 Totals 209 259 485 1,295 614 466 275 1,879 793 1,591 1,495 637 256 1,622 715 2,185 1,022 2,759 1,087 804 394 2,239 1,281 Redd /holding fish ratio 1.7 2.4 1.1 2.5 2.3 2.1 2.5 2.0 1.7 35

Appendix Table A18. Chinook salmon mark-and-recovery data used to estimate the 2005 fall-run spawner population in Deer Creek from the USGS gauging station downstream to the Highway 99 Bridge, using Chapman s version of the Peterson equation. Survey Period Marked Carcasses Total Carcasses Recovered Carcasses 14-21 Nov 56 75 0 1-9 Dec 0 326 26 15 Dec 0 54 0 Totals 56 455 26 N= 946 Where: N=Estimated Spawner Population=(M+1)(C+1)/R+1 (Ricker 1975) M=number of carcasses marked C=number of carcasses observed, including those marked and those recovered with marks R=number of marked carcasses recovered. 36

APPENDIX B (Coded-Wire-Tag Results Tables) Appendix Table B1. Summary of the Coded-wire-tag (CWT) results, by brood year, for adipose-fin clipped (hatchery) Chinook salmon in the Upper Sacramento River Basin in 2005 collected during Sacramento River Salmon and Steelhead Assessment Project escapement surveys. Brood Year Battle Clear Deer Mill Sac. Riv. Totals Age Percent 2003 4 0 0 0 75 79 2 year old 5.2% 2002 15 5 0 1 1,306 1,327 3 year old 87.2% 2001 48 6 0 2 56 112 4 year old 7.4% 2000 2 0 0 0 2 4 5 year old 0.3% No tag data 17 5 1 1 327 351 unknown Totals 86 16 1 4 1,766 1,873 100.0% Appendix Table B2. Summary of the 2005 CWT results, by run, for adipose-fin clipped (hatchery) Chinook salmon in the Upper Sacramento River Basin collected during Sacramento River Salmon and Steelhead Assessment Project escapement surveys. Location Spring ^ Fall Winter Late-Fall Totals Battle Creek 0 67 0 2 69 Clear Creek 0 11 0 0 11 Deer Creek 0 0 0 0 0 Mill Creek 0 3 0 0 3 Sacramento 13 23 1,272 131 1,439 Totals 13 104 1,272 133 1,522 ^ Spring-run CWT data are salmon from the Feather River Hatchery 37

Appendix Table B3. Summary of the 2005 CWT results, by hatchery, for adipose-fin clipped (hatchery) Chinook salmon in the Upper Sacramento River Basin collected during Sacramento River Salmon and Steelhead Assessment Project escapement surveys. HATCHERY SOURCE Total Percentage LIVINGSTON STONE NFH 1,272 83.6% COLEMAN NFH 225 14.8% FEATHER R HATCHERY 17 1.1% MERCED R FISH FACIL. 4 0.3% MOKELUMNE R FISH INS 4 0.3% CWT's with good reads: Total 1,522 100.0% TAG NOT DETECTED (100000) 313 TAG LOST (200000) 7 0.5% HEAD NOT RECOVERED (300000) 0 TAG ILLEGIBLE (400000) 7 0.5% Total Problem CWT's 327 % of total Overall CWT (found) Totals 1,536 found cwt 38

Appendix Table B4. Summary of the 2005 CWT results, by tag code, for adipose-fin clipped (hatchery) Chinook salmon in the Upper Sacramento River Basin collected during Sacramento River Salmon and Steelhead Assessment Project escapement surveys. CWT Code Hatchery* Release Location Brood Year Run Battle Clear Deer Mill Sac Riv. 50399 CNFH Battle creek 2000 Late-Fall 1 50468 CNFH Battle creek 2000 Late-Fall 1 50568 CNFH Battle creek 2000 Fall 1 50766 CNFH Battle creek 2001 Late-Fall 1 50767 CNFH Ryde-Koket 2001 Late-Fall 12 50768 CNFH Port Chicago 2001 Late-Fall 1 50769 CNFH Battle creek 2001 Late-Fall 4 50770 CNFH Battle creek 2001 Late-Fall 4 50771 CNFH Battle creek 2001 Late-Fall 4 50772 CNFH Battle creek 2001 Late-Fall 6 50773 CNFH Battle creek 2001 Late-Fall 2 50774 CNFH Battle creek 2001 Late-Fall 2 50775 CNFH Battle creek 2001 Late-Fall 1 50776 CNFH Georgianna Sl. 2001 Late-Fall 1 50874 CNFH CNFH 2001 Fall 1 50875 CNFH CNFH 2001 Fall 2 50876 CNFH CNFH 2001 Fall 2 1 50877 CNFH CNFH 2001 Fall 1 50878 CNFH CNFH 2001 Fall 3 1 50879 CNFH CNFH 2001 Fall 2 50880 CNFH CNFH 2001 Fall 4 50881 CNFH CNFH 2001 Fall 4 50882 CNFH CNFH 2001 Fall 2 1 50883 CNFH CNFH 2001 Fall 1 50884 CNFH CNFH 2001 Fall 4 50885 CNFH CNFH 2001 Fall 2 50886 CNFH CNFH 2001 Fall 1 50887 CNFH CNFH 2001 Fall 1 51091 CNFH CNFH 2002 Late-Fall 5 51092 CNFH CNFH 2002 Late-Fall 2 51093 CNFH CNFH 2002 Late-Fall 10 51094 CNFH CNFH 2002 Late-Fall 2 51095 CNFH CNFH 2002 Late-Fall 3 51096 CNFH CNFH 2002 Late-Fall 7 51099 CNFH CNFH 2002 Late-Fall 11 51164 CNFH CNFH 2002 Late-Fall 10 51165 CNFH CNFH 2002 Late-Fall 5 51166 CNFH Port Chicago 2002 Late-Fall 6 51167 CNFH Ryde-Koket 2002 Late-Fall 4 51276 LNFH Lk. Redding Pk. 2002 Winter 24 39

CWT Code Hatchery* Release Location Brood Year Run Battle Clear Deer Mill Sac Riv. 51277 LNFH Lk. Redding Pk. 2002 Winter 34 51278 LNFH Lk. Redding Pk. 2002 Winter 35 51279 LNFH Lk. Redding Pk. 2002 Winter 25 51280 LNFH Lk. Redding Pk. 2002 Winter 17 51281 LNFH Lk. Redding Pk. 2002 Winter 28 51282 LNFH Lk. Redding Pk. 2002 Winter 51 51283 LNFH Lk. Redding Pk. 2002 Winter 22 51284 LNFH Lk. Redding Pk. 2002 Winter 34 51285 LNFH Lk. Redding Pk. 2002 Winter 26 51286 LNFH Lk. Redding Pk. 2002 Winter 37 51287 LNFH Lk. Redding Pk. 2002 Winter 23 51288 LNFH Lk. Redding Pk. 2002 Winter 28 51289 LNFH Lk. Redding Pk. 2002 Winter 26 51290 LNFH Lk. Redding Pk. 2002 Winter 38 51291 LNFH Lk. Redding Pk. 2002 Winter 28 51292 LNFH Lk. Redding Pk. 2002 Winter 17 51293 LNFH Lk. Redding Pk. 2002 Winter 34 51294 LNFH Lk. Redding Pk. 2002 Winter 35 51295 LNFH Lk. Redding Pk. 2002 Winter 8 51296 LNFH Lk. Redding Pk. 2002 Winter 62 51297 LNFH Lk. Redding Pk. 2002 Winter 72 51298 LNFH Lk. Redding Pk. 2002 Winter 109 51299 LNFH Lk. Redding Pk. 2002 Winter 29 51364 LNFH Lk. Redding Pk. 2002 Winter 19 51365 LNFH Lk. Redding Pk. 2002 Winter 23 51366 LNFH Lk. Redding Pk. 2002 Winter 31 51367 LNFH Lk. Redding Pk. 2002 Winter 25 51368 LNFH Lk. Redding Pk. 2002 Winter 29 51369 LNFH Lk. Redding Pk. 2002 Winter 47 51370 LNFH Lk. Redding Pk. 2002 Winter 29 51371 LNFH Lk. Redding Pk. 2002 Winter 35 51372 LNFH Lk. Redding Pk. 2002 Winter 35 51373 LNFH Lk. Redding Pk. 2002 Winter 25 51679 LNFH Lk. Redding Pk. 2003 Winter 1 51699 CNFH CNFH 2003 Late-Fall 1 3 51764 CNFH CNFH 2003 Late-Fall 1 51766 CNFH CNFH 2003 Late-Fall 1 51770 CNFH CNFH 2003 Late-Fall 1 51775 CNFH CNFH 2003 Late-Fall 1 51780 CNFH Benicia 2003 Late-Fall 2 51964 LNFH Lk. Redding Pk. 2003 Winter 3 51970 LNFH Lk. Redding Pk. 2003 Winter 3 51971 LNFH Lk. Redding Pk. 2003 Winter 1 51972 LNFH Lk. Redding Pk. 2003 Winter 1 51973 LNFH Lk. Redding Pk. 2003 Winter 7 51974 LNFH Lk. Redding Pk. 2003 Winter 8 40

CWT Code Hatchery* Release Location Brood Year Run Battle Clear Deer Mill Sac Riv. 51977 LNFH Lk. Redding Pk. 2003 Winter 1 51978 LNFH Lk. Redding Pk. 2003 Winter 3 51980 LNFH Lk. Redding Pk. 2003 Winter 1 51982 LNFH Lk. Redding Pk. 2003 Winter 1 51983 LNFH Lk. Redding Pk. 2003 Winter 1 51984 LNFH Lk. Redding Pk. 2003 Winter 3 51985 LNFH Lk. Redding Pk. 2003 Winter 1 51986 LNFH Lk. Redding Pk. 2003 Winter 3 51988 LNFH Lk. Redding Pk. 2003 Winter 2 51991 LNFH Lk. Redding Pk. 2003 Winter 2 51993 LNFH Lk. Redding Pk. 2003 Winter 3 51995 LNFH Lk. Redding Pk. 2003 Winter 5 51996 LNFH Lk. Redding Pk. 2003 Winter 10 51997 LNFH Lk. Redding Pk. 2003 Winter 7 53737 LNFH Lk. Redding Pk. 2002 Winter 64 55135 CNFH Battle creek 2001 Late-Fall 2 55138 CNFH West Sacto. 2002 Late-Fall 5 55139 CNFH CNFH 2002 Late-Fall 11 62090 FRH Wickland net pen 2001 Fall 1 62091 FRH Wickland net pen 2001 Fall 1 62744 MRFF Jersey Pt. 2002 Fall 1 62756 FRH Benicia 2002 Spring 3 62758 FRH Benicia 2002 Spring 2 62759 FRH Benicia 2002 Spring 1 62761 FRH Benicia 2002 Spring 1 62762 FRH Benicia 2002 Spring 1 62763 FRH Benicia 2002 Spring 2 62764 FRH Live Oak 2002 Fall 1 62774 FRH Crockett 2002 Fall 1 62785 FRH Benicia 2002 Spring 3 64460 MRFF Jersey Pt. 2001 Fall 1 64480 MRFF Jersey Pt. 2001 Fall 1 64481 MRFF Jersey Pt. 2001 Fall 1 64925 MRFI Mok. Riv, Staten Isl. 2001 Fall 1 64930 MRFI Sherman Isl-Jersey 2001 Fall 2 64931 MRFI Sherman Isl-Jersey 2001 Fall 1 501020103 CNFH Clarksburg 2002 Fall 1 501020104 CNFH RBDD 2002 Fall 8 3 1 501020106 CNFH RBDD 2002 Fall 7 2 4 501030507 CNFH Battle creek 2000 Fall 1 501030707 LNFH Lk. Redding Pk. 2001 Winter 1 501040105 CNFH CNFH 2001 Fall 2 501040106 CNFH CNFH 2001 Fall 1 501040108 CNFH Battle creek 2003 Fall 1 501040109 CNFH Battle creek 2003 Fall 1 501040201 CNFH CNFH 2001 Fall 3 41

CWT Code Hatchery* Release Location Brood Year Run Battle Clear Deer Mill Sac Riv. 501040202 CNFH CNFH 2001 Fall 1 501040203 CNFH CNFH 2001 Fall 3 1 1 501040204 CNFH CNFH 2001 Fall 2 1 501040206 CNFH CNFH 2001 Fall 1 1 501040207 CNFH CNFH 2001 Fall 2 501040208 CNFH CNFH 2001 Fall 1 501040209 CNFH CNFH 2001 Fall 3 501040301 CNFH RBDD 2001 Fall 1 501040302 CNFH Clarksburg 2001 Fall 1 501040303 CNFH RBDD 2001 Fall 2 2 100000 No Tag No tag detected Fall 17 5 1 1 11 100000 No Tag No tag detected Late-Fall 19 100000 No Tag No tag detected Winter 283 200000 Tag Lost Tag Lost Winter 7 400000 Illegible Tag Scratched Late-Fall 7 TOTALS 86 16 1 4 1,766 Carcasses examined for ad-clips: These numbers are for general categories; for specific analysis purposes please contact Project biologists 10,258 5619 485 1114 17,162 Chinook Population estimates (tributaries fall-run only) 20,520 14,824 946 2485 83,452 * Hatchery Abbreviations as follows: CNFH = Coleman National Fish Hatchery LSNFH = Livingston Stone National Fish Hatchery MRFI = Mokelumne River Fish Installation FRH = Feather River Hatchery MRFF = Merced River Fish Facility 42

APPENDIX C (Data Figures) 75.0 Temperature F 70.0 65.0 60.0 55.0 50.0 68 F partial egg mortality 63.5 F reduced egg viability 59 F normal egg viability 45.0 40.0 5/1 5/13 5/25 6/6 6/18 6/30 7/12 7/24 8/5 8/17 8/29 9/10 9/22 10/4 10/16 10/28 North South (1400 ft elev.) Paynes Crossing (1300 ft elev.) Appendix Figure C1. Average daily water temperature and salmon tolerance limits in Antelope Creek SRCS habitat, 2005. 1200 20 1100 1000 900 800 peak migration timing 18 16 14 flow (cfs) 700 600 500 400 300 200 12 10 8 6 4 % migrate 100 estimated minimum migration flows 2 0 3/1/2005 3/15/2005 3/29/2005 4/12/2005 4/26/2005 5/10/2005 5/24/2005 6/7/2005 6/21/2005 7/5/2005 Date 0 %migrate MCH (cfs), post-diversions MLM (cfs), pre-diversions Appendix Figure C2. Average daily water flow and SRCS migration timing in Mill Creek, March June, 2005. 43

75.0 70.0 migration tolerance limit 65.0 60.0 Temperature (F) 55.0 50.0 45.0 40.0 35.0 30.0 3/1/2005 3/15/2005 3/29/2005 4/12/2005 4/26/2005 5/10/2005 5/24/2005 6/7/2005 6/21/2005 MLM pre-divert MCH post-divert Appendix, Figure C3. Average daily water temperature and migration tolerance limits during adult SRCS migration in Mill Creek, March June, 2006. 80.0 75.0 Temperature F 70.0 65.0 60.0 55.0 50.0 68 F partial egg mortality 6 v 5 v 45.0 40.0 35.0 30.0 5/1/2005 5/13/2005 5/25/2005 6/6/2005 6/18/2005 6/30/2005 7/12/2005 7/24/2005 8/5/2005 8/17/2005 8/29/2005 9/10/2005 9/22/2005 10/4/2005 10/16/2005 10/28/2005 Hwy. 36 Hole-in-Ground Sooner's Blackrock Rancheria Little Mill Appendix Figure C4. Average daily water temperatures and salmon tolerance limits in Mill Creek in SRCS habitat, May October, 2006. 44

1500 80.0 1400 1300 1200 1100 maximum temperature tolerance 70.0 60.0 flow (cfs) 1000 900 800 700 600 500 400 300 200 50.0 40.0 30.0 20.0 10.0 water temp (F) 100 0 10/1/2005 10/11/2005 10/21/2005 10/31/2005 11/10/2005 11/20/2005 minimum migration flow range 11/30/2005 12/10/2005 12/20/2005 12/30/2005 0.0 pre-divert flow post divert flow pre-divert temp. post-divert temp. Appendix Figure C5. Average daily flow and water temperature in Mill Creek during FRCS spawning, October December, 2005. flow (cfs) 900 800 700 600 500 400 300 200 100 0 migration tolerance limit minimum migration flow range 4/1/2005 4/8/2005 4/15/2005 4/22/2005 4/29/2005 5/6/2005 5/13/2005 5/20/2005 5/27/2005 6/3/2005 6/10/2005 6/17/2005 6/24/2005 90.0 80.0 70.0 60.0 50.0 40.0 30.0 20.0 10.0 0.0 Temperature (F) pre-divert Flow post-divert flow pre-divert Water Temp post-divert Water temp Appendix Figure C6. Average daily water flow, temperature and salmon tolerance limits during adult SRCS migration in Deer Creek, April June, 2005. 45

75.0 70.0 65.0 Temperature (F) 60.0 55.0 50.0 45.0 40.0 6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 Spring-Run Holding and Spawning Period Upper Falls Pool Upper Falls Riffle Wilson Cove 2E17 Ponderosa Way Murphy Trail Lower Falls Appendix Figure C7. Average daily water temperature and adult salmon tolerance limits in Deer Creek SRCS habitat, May October, 2005. 900 80.0 flow (cfs) 800 700 600 500 400 300 200 100 maximum temperature tolerance 70.0 60.0 50.0 40.0 30.0 20.0 10.0 Temperature (F) 0 0.0 10/1/2005 10/15/2005 10/29/2005 11/12/2005 11/26/2005 12/10/2005 12/24/2005 pre-diverted flow post-diverted flow post-diverted Water Temp pre-diverted Water Temp Appendix Figure C8. Average daily water flow, temperature and adult salmon tolerance limits in Mill Creek during FRCS spawning, October November, 2005. 46