Fishery Analysis for the Carmel River Lagoon Biological Assessment Report March 2014 Prepared By: P.O. Box 200, Brookdale, CA 95007 Prepared For: Monterey County Resource Management Agency Monterey County Government Center 168 W. Alisal Street, 2nd Floor Salinas, CA 93901 TABLE OF CONTENTS INTRODUCTION ........................................................................................................................................ 1 Project History .......................................................................................................................................... 1 Memorandum of Understanding ......................................................................................................... 4 Project Description .................................................................................................................................... 5 EPB Components ................................................................................................................................. 6 SRPS Components ............................................................................................................................... 6 ISMP Components ............................................................................................................................... 6 Project Action Area ................................................................................................................................... 8 STUDY METHODS ..................................................................................................................................... 9 Listed Fish Species.................................................................................................................................... 9 ENVIRONMENTAL SETTING ................................................................................................................ 10 Impacts of Historical Mechanical Breaching .......................................................................................... 10 Benefits of a Natural Breaching Regime ................................................................................................ 11 Steelhead Occurrences in the Project Area ............................................................................................. 12 Adult Migration .................................................................................................................................. 13 Spawning ............................................................................................................................................ 17 Summer Rearing ................................................................................................................................ 17 Smolt Migration ................................................................................................................................. 18 Physical and Biological Aspects of the Carmel Lagoon/Estuary Pertaining to Steelhead Habitat and Rational for Assessing Impacts of Proposed Actions ............................................................................. 24 Food Web ........................................................................................................................................... 24 Water Temperature ............................................................................................................................ 24 Oxygen Levels .................................................................................................................................... 25 Discussion of Critical Environmental Factors ................................................................................. 26 DISCUSSION OF SOUTH-CENTRAL CALIFORNIA COAST STEELHEAD DPS ............................. 36 Survey Results ........................................................................................................................................ 36 Critical Habitat ........................................................................................................................................ 36 Avoidance and Minimization Efforts ...................................................................................................... 36 Project Effects ......................................................................................................................................... 38 EPB ..................................................................................................................................................... 38 SRPS ................................................................................................................................................... 39 ISMP ................................................................................................................................................... 40 Project Impacts ........................................................................................................................................ 40 Impacts potentially resulting from the EPB: .................................................................................... 40 Impacts potentially resulting from the SRPS .................................................................................... 41 Impacts potentially resulting from the ISMP .................................................................................... 41 Modifications to the Project to Mitigate Potentially Negative Effects ................................................... 42 Monitoring and Reporting ....................................................................................................................... 44 DRAFT Fishery Analysis for The Carmel River Lagoon Biological Assessment Report− January 2014 D.W. ALLEY & Associates Page i Reporting Recommendations ............................................................................................................. 46 Cumulative Effects (ESA) ...................................................................................................................... 46 CONCLUSIONS AND DETERMINATIONS ........................................................................................... 47 Conclusions ............................................................................................................................................. 47 Determination.......................................................................................................................................... 47 LITERATURE CITED ............................................................................................................................... 48 LIST OF CONTACTS AND PERSONAL COMMUNICATIONS ........................................................... 52 APPENDIX A: Interim Sandbar Management Plan (ISMP) APPENDIX B: California Department of Fish and Game Avoidance and Minimization Measures DRAFT Fishery Analysis for The Carmel River Lagoon Biological Assessment Report− January 2014 D.W. ALLEY & Associates Page ii FIGURES Figure 1. Project Location ............................................................................................................................. 2 Figure 2. Project Components ....................................................................................................................... 7 Figure 3. Steelhead Occurrences Within the Vicinity ................................................................................. 37 CHARTS Chart 1. Carmel River Mean Daily Flow at First Mechanical Breach of Sandbar Barrier, 1993─2012. Data from Balance Hydrologics Technical Memorandum (2013). .............................................. 16 Chart 2. Actual Daily and Cumulative Smolt Catch Over Time Below Los Padres Dam, 1999. ................ 20 Chart 3. MPWMD Steelhead Smolt Trapping – Scarlett Site, 2007. ........................................................... 21 Chart 4. MPWMD Steelhead Smolt Trapping – Scarlett Site, 2013. ........................................................... 21 Chart 5. San Lorenzo River Smolt Trapping, 1987. .................................................................................... 22 Chart 6. San Lorenzo River Smolt Trapping, 1988. .................................................................................... 22 Chart 7. Morning Oxygen Levels and Gage Heights in the Central Embayment of the Carmel Lagoon/Estuary, 2005. ................................................................................................................. 29 Chart 8. Morning Oxygen Levels and Gage Heights in the South Arm of the Carmel Lagoon/Estuary, 2005. ............................................................................................................................................. 30 Chart 9. Morning Oxygen Levels and Gage Heights in the North Arm of the Carmel Lagoon/Estuary, 2005. ............................................................................................................................................. 31 Chart 10. Morning Water Temperature and Gage Heights in the Central Embayment of the Carmel Lagoon/Estuary, 2005. ................................................................................................................. 32 Chart 11. Morning Water Temperature and Gage Heights in the South Arm of the Carmel Lagoon/Estuary, 2005. ................................................................................................................. 33 Chart 12. Morning Water