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Evaluation of Coho and Steelhead Production in the San Geronimo Valley Headwaters of the Lagunitas Creek Watershed, 2006-2008

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Evaluation of Coho and Steelhead Production in the San Geronimo Valley Headwaters of the Lagunitas Creek Watershed, 2006-2008 Evaluation of Coho and Steelhead Production in the San Geronimo Valley Headwaters of the Lagunitas Creek Watershed, 2006-2008 Prepared by Christopher Pincetich, Ph.D., SPAWN Watershed Biologist Todd Steiner, M.S., SPAWN Executive Director Paola Bouley, M.S., SPAWN Conservation Program Director Ssssssssssssssssss Salmon Protection Salmon Protection And Watershed Network And Watershed PO Box 370 • Forest Knolls, CA 94933 Network Ph. 415.663.8590 • Fax 415.663.9534 PO Box 400 • Forest www.SpawnUSA.org Knolls, CA 94933 i Salmon Protection and Watershed Network (SPAWN) Evaluation of Coho and Steelhead Production in the San Geronimo Valley Headwaters of the Lagunitas Creek Watershed, 2006-2008 Table of Contents Abstract…………………………………………………………………………………………………...…1 Introduction……………………………………………………………….…………………….…………...1 Lagunitas Coho………………………………………….…………………………..……...…...1 Lagunitas Steelhead………………………………………….…………………….….…….....2 San Geronimo Valley Headwaters………………………………………….….………….....2 Salmon Protection and Watershed Network (SPAWN)………………...…..…………....2 Methods……………………………………………………………………………………………..…...…4 Smolt Trap Design and Location ………………………………………………...……...….4 Daily Monitoring………………………………………………………………………..…..……5 Data Analyses………………………………………………………………………………...…6 Fulton Condition Factor……………………………………………………………..……..…..6 Results……………………………………………………………………………………..……...….….…6 Coho Salmon………………………………………………………………………..…..…….…7 Steelhead……………………………………..……………………………………..…..………10 Other Aquatic Organisms ……………………………………..……………………..…...…14 Discussion……………………………………………………………………………………….……...…15 Acknowledgements…………………………………………………………………………….…………17 References……………………………………………………………………………………………...…18 List of Tables Table 1. Summary of coho smolt population estimates from San Geronimo Valley (SGV) and total Lagunitas Creek Watershed (LCW)…………………………….………………………...………...……6 Table 2. Summary of coho smolt measurements from the San Geronimo Creek monitoring station………………………………………………………………………………………………………..7 Table 3. Table 2. Summary of steelhead smolt population estimates from San Geronimo Valley (SGV) and total Lagunitas Creek Watershed (LCW). ………………………………..…..……..……11 Table 4. Summary of measurements from San Geronimo Creek steelhead smolts with smoltification code 4. …………………………..…………………..…………………………...….……11 Table 5. Summary of measurements from San Geronimo Creek steelhead juveniles with smoltification codes 2-3. ……………..…………………………………………….……………..……..11 Table 6. Summary counts of non-salmonid species recovered in smolt traps……………………..14 Table 7. Summary of average coho smolt fork lengths from SPAWN (SGV), MMWD (Lagunitas), and NPS (Olema and Redwood Creeks) ……………………………………………………………...16 ii Salmon Protection and Watershed Network (SPAWN) Table 8. Summary of new coho smolt physiology from Lagunitas Creek Watershed (LCW; MMWD data). ……………………………………………………………………………………………….……...16 Table 9. Summary of marked, recaptured SGV coho smolt physiology as measured at downstream LCW monitoring station. ……………………………………………………………..…...16 Table 10. Summary of marked, recaptured LCW coho smolt physiology as measured at downstream LCW monitoring station. ……………………………………………………………..…...16 List of Figures Figure 1. The Lagunitas Creek watershed is located north of San Francisco Bay in Marin County, California, and originates near the top of Mount Tamalpias and flows north to Tomales Bay. The San Geronimo Creek watershed is the upper, un-dammed headwater tributary that joins Lagunitas Creek 7.2 km downstream from its origins on White’s Hill…...……………………………3 Figure 2. The San Geronimo Valley sub-watershed contains twelve main tributaries that currently support coho salmon or steelhead. The location of the three outmigrant smolt monitoring stations are shown along San Geronimo, Arroyo, and Larsen Creeks.…………………………………....…4 Figure 3. The smolt traps were constructed as a combination fyke net/pipe trap design intended for larger creeks (A). Smolts were measured (B) and weighed (C) while immersed in cold creek water to minimize handling stress. …………………………………………………………………….…5 Figure 4. Outmigrant coho smolt captures, capture probability, and population estimates from 2006 monitoring in San Geronimo Creek………………………………………………………….….…7 Figure 5. Salmonid measurements from 2006 San Geronimo Creek monitoring of fork length and wet weight plotted for coho smolts………………………………………………………………………..8 Figure 6. Outmigrant coho smolt captures, capture probability, and population estimates from 2007 monitoring in San Geronimo Creek……………………………………………...……….…….….8 Figure 7. Salmonid measurements from 2007 San Geronimo Creek monitoring of fork length and wet weight plotted for coho smolts ……………………………………………………………………….9 Figure 8. Outmigrant coho smolt captures, capture probability, and population estimates from 2008 monitoring in San Geronimo Creek……………………………………………………….....…….9 Figure 9. Coho smolt weekly average length and abundance in San Geronimo Creek in 2008…10 Figure 10. Salmonid measurements from 2008 San Geronimo Creek monitoring of fork length and wet weight plotted for coho smolts ………………………………………………………..………10 Figure 11. Outmigrant steelhead smolt captures, capture probability, and population estimates from 2006 monitoring in San Geronimo Creek……………………………………………….…..……11 Figure 12. Steelhead smolt and parr measurements of fork length vs. wet weight plotted from 2006 San Geronimo Creek monitoring…………………………..……………………………….….…12 Figure 13. Outmigrant steelhead smolt captures, capture probability, and population estimates from 2007 monitoring in San Geronimo Creek…………………………………….………….….…...12 iii Salmon Protection and Watershed Network (SPAWN) Figure 14. Steelhead smolt and parr measurements of fork length vs. wet weight plotted from 2007 San Geronimo Creek monitoring…………………………..…………………………..…………13 Figure 15. Outmigrant steelhead smolt captures, capture probability, and population estimates from 2008 monitoring in San Geronimo Creek………………………………………………..……….13 Figure 16. Steelhead smolt weekly average length and abundance in San Geronimo Creek in 2008…………………………………………………………………………………………………..…....14 Figure 17. Steelhead smolt and parr measurements of fork length vs. wet weight plotted from 2008 San Geronimo Creek monitoring…………………………..…………………………..…………14 iv Abstract The San Geronimo Valley (SGV) sub-watershed is a 10 square-mile headwaters region in the Lagunitas Creek Watershed (LCW) of Marin County, California. The LCW supports the largest documented wild population of endangered Central Coast ESU coho salmon and is also home to the 2nd largest population of threatened CCC ESU steelhead. Smolt production of coho salmon and steelhead in the SGV was determined through outmigrant monitoring during the spring months of 2006 - 2008 by the Salmon Protection and Watershed Network (SPAWN). SPAWN biologists made daily observations and measurements at three fyke-net fish traps and used a consistent mark and recapture strategy to estimate the number of coho salmon or steelhead smolts migrating toward the ocean. These headwaters monitoring efforts were done in coordination with efforts downstream on lower Lagunitas Creek at a trap operated by the Marin Municipal Water District (MMWD). Coho smolt captures and population estimates were larger each year than those for steelhead in the SGV, and average coho smolt fork length declined each year of monitoring. In 2008, average weekly fork length measurements were compared and there was no significant difference in smolt size during the individual weeks of the outmigration period for either coho or steelhead. Overall, average coho smolt size in the SGV was smaller than that observed at the downstream Lagunitas trap each year, but analyses of SGV smolts recaptured downstream revealed that the average size of these fish had increased during downstream migration to very near the average recaptured downstream smolts. The smolt population in both SGV and LCW was lowest in 2007, which correlates to low juveniles population estimates in the summer of 2006 caused by the highest flows recorded since 1982 during the new year eve’s storm of 2005/06. For the period of monitoring by both SPAWN and MMWD from 2006-2008, the SGV, which is less than 9% of the total LCW, supported 24%- 53% of the total LCW estimated coho smolt population, validating the importance of continued habitat conservation, restoration and monitoring efforts in this area. Introduction The Lagunitas Creek watershed (LCW) of Marin County supports the largest-remaining documented wild population of endangered Central Coast coho salmon (Oncorhynchus kisutch) in California (Moyle et al., 2008). The Central California Coast Evolutionarily Significant Unit (ESU) of coho salmon has been listed as endangered in the State of California and under the U.S. Endangered Species Act (ESA) since 2005. The SGV also supports a population of Central California Coast ESU steelhead (Oncorhynchus mykiss) that has been listed at threatened under the ESA since 2006. Lagunitas Coho The LCW occupies 281.85 km2 (69,646 acres) in Marin County Ca, and contains 56.32km (35 miles) of endangered coho salmon coho bearing streams and 59.55km (37 miles) of threatened steelhead streams (NOAA SWFS, 2008), including Lagunitas Creek, Devil’s Gulch Creek, and San Geronimo Creek and its tributaries. Coho salmon essentially have a fixed three-year life cycle, and for coho, a separate year class is created every three years and can be considered essentially a separate population because there is little mixing among year class lineages. The exception can be the occurrence of
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