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D.W. ALLEY & Associates Aquatic Biology

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D.W. ALLEY & Associates Aquatic Biology D.W. ALLEY & Associates Aquatic Biology -------------------------------------------------------------------------- 2006 Juvenile Steelhead Densities in the San Lorenzo, Soquel, Aptos and Corralitos Watersheds, Santa Cruz County, California Coastrange Sculpin Photographed by Jessica Wheeler D.W. ALLEY & Associates, Aquatic Biology Don Alley, Chad Steiner and Jerry Smith, Fishery Biologists With Field Assistance from Kristen Kittleson, Dawn Reis and Jessica Wheeler Prepared For the Santa Cruz County Environmental Health Department Government Center, 701 Ocean Street, Room 312, Santa Cruz, CA 95060 Funding From the San Lorenzo Valley Water District, Soquel Creek Water District, Lompico County Water District, Cities of Santa Cruz and Watsonville and the County of Santa Cruz May 2007 Project # 200-04 340 Old River Lane • P.O. Box 200 • Brookdale, California 95007 • (831) 338-7971 TABLE OF CONTENTS REPORT SUMMARY...................................................................................10 INTRODUCTION..........................................................................................31 I-1. Steelhead and Coho Salmon Ecology...................................................... 31 I-3. Project Purpose and General Study Approach ........................................ 34 METHODS ....................................................................................................35 M-1. Choice of Reaches and Vicinity of Sites to be Sampled- Methods........... 35 M-2. Classification of Habitat Types and Measurement of Habitat Characteristics.............................................................................................. 38 M-3. Measurement of Habitat Parameters..................................................... 38 M-4. Choice of Specific Habitats Within Reaches to be Sampled- Methods .... 41 M-5. Consistency of Data Collection Techniques in 1994-2001 and 2003-2006 ..................................................................................................................... 42 M-6. Juvenile Steelhead Densities at Sampling Sites - Methods...................... 54 M-7. Capture and Mortality Statistics............................................................ 56 M-8. Age and Size Class Divisions ................................................................ 56 RESULTS......................................................................................................58 R-1. Habitat Change in the San Lorenzo River and Tributaries..................... 58 R-2. Habitat Change in Soquel Creek and Its Branches ................................ 60 R-3. Habitat Change in Aptos and Valencia Creeks ...................................... 61 R-4. Trends in Habitat Change in Corralitos, Shingle Mill and Browns Valley Creeks........................................................................................................... 62 STEELHEAD DENSITY COMPARISONS ....................................................80 R-5. Comparison of 2006 Steelhead Densities in the San Lorenzo Drainage with Those Since 1997.......................................................................................... 80 R-6. Comparison of 2006 Steelhead Densities in Soquel Creek with Those Since 1997............................................................................................................. 80 R-7. Comparison of 2006 Steelhead Densities in Aptos and Valencia Creeks with Those in 1981 and 1994............................................................................... 81 R-8. Comparison of 2006 Steelhead Densities in Corralitos, Browns Valley and Shingle Mill with those in 1981 and 1994..................................................... 81 R-9. Rating of Smolt Rearing Habitat in 2006, Based on Site Densities of Smolt-Sized Fish ..........................................................................................102 R-10. Statistical Analysis of Annual Differences in Juvenile Steelhead Densities D.W. ALLEY & Associates Santa Cruz County Fishery Report 2006 P.O. Box 200 • Brookdale, California 95007 1 ....................................................................................................................104 R-11. Adult Trapping Results at the Fish Ladder on the Felton Diversion Dam ....................................................................................................................105 DISCUSSION..............................................................................................108 D-1. Comparisons of the Annual Trend in Young-of-the-Year and Yearling Steelhead Densities in Santa County Streams with Trends in Other Coastal Streams........................................................................................................108 D-2. Causal Factors for Average or Above Size Class II/III (Smolt-Sized) Juvenile Steelhead Densities in 2006 and Lower Total Densities Compared to Previous Years in the San Lorenzo and Soquel Watersheds...........................108 D-3. Causal Factors for Similar or Higher Total and Size Class II/ III (Smolt- Sized) Juvenile Steelhead Densities in 2006 Compared to Previous Sampling in Corralitos and Aptos Creeks.........................................................................109 D-4. Data Gaps...........................................................................................111 CONCLUSIONS..........................................................................................113 C-1. Habitat Conditions in 2006 Compared to Previous Years .....................113 C-2. Comparison of 2006 Steelhead Densities with Past Results...................115 C-3. Statistical Comparison of 2005 and 2006 Steelhead Densities.............116 REFERENCES AND COMMUNICATIONS ................................................117 FIGURES ....................................................................................................120 APPENDIX A. Maps of Sampling Sites........................................................155 APPENDIX B. Summary of Catch Data for Sampling Sites...........................163 APPENDIX C. Habitat and Fish Sampling Data With Size Histograms............200 D.W. ALLEY & Associates Santa Cruz County Fishery Report 2006 P.O. Box 200 • Brookdale, California 95007 2 LIST OF TABLES Table 1a. Defined Reaches in the Mainstem San Lorenzo River.....................................................................................43 Table 1b. Defined Reaches in Major Tributaries of the San Lorenzo River. ................................................................44 Table 2a. Defined Reaches on Soquel Creek.......................................................................................................................48 Table 2b. Locations of Sampling Sites by Reach on Soquel Creek.................................................................................50 Table 3. Locations of Sampling Sites by Reach in the Aptos Watershed.......................................................................51 Table 4a. Defined Reaches in the Corralitos Sub-Watershed. ........................................................................................52 Table 4b. Locations of Sampling Sites by Reach in the Corralitos Sub-Watershed....................................................54 Table 5. Fall STREAMFLOW (cubic feet/ sec) Measured by Flowmeter at SAN LORENZO Sampling Sites........63 Table 6. Averaged Mean and Maximum WATER DEPTH (ft) of Habitat in SAN LORENZO Reaches Since 2000.64 Table 7. Average PERCENT FINE SEDIMENT IN SAN LORENZO Reaches River Since 2000...............................66 Table 8. Average EMBEDDEDNESS IN SAN LORENZO Reaches Since 2000............................................................67 Table 9. Reach-wide ESCAPE COVER Index (Habitat Typing Method*) in RIFFLE HABITAT in MAINSTEM Reaches of the SAN LORENZO, Based on Habitat Typed Segments..............................................................................68 Table 10. Reach-wide ESCAPE COVER Index (Habitat Typing Method*) in RUN HABITAT in MAINSTEM Reaches of the SAN LORENZO, Based on Habitat Typed Segments..............................................................................69 Table 11. ESCAPE COVER Index (Habitat Typing Method*) in Pool Habitat in MAINSTEM Reaches of the SAN LORENZO, Based on Habitat Typed Segments...................................................................................................................70 Table 12. ESCAPE COVER Index (Habitat Typing Method*) for POOL HABITAT in TRIBUTARY Reaches of the SAN LORENZO.........................................................................................................................................................................71 Table 13. ESCAPE COVER Index (Habitat Typing Method*) for RUN HABITAT in TRIBUTARY Reaches of the SAN LORENZO.........................................................................................................................................................................72 Table 14. Averaged Mean and Maximum WATER DEPTH (ft) of Habitat in SQOUEL CREEK Reaches Since 2000. .......................................................................................................................................................................................................73 D.W. ALLEY & Associates Santa Cruz County Fishery Report 2006 P.O. Box 200 • Brookdale, California 95007 3 Table 15. Average PERCENT FINE SEDIMENT in Habitat-typed Reaches in SOQUEL CREEK Since 2000.........74 Table 16. Average EMBEDDEDNESS in
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