Stockton and Sacramento Deepwater Ship Channel Maintenance Dredging Project 2009 Fish Community and Entrainment Monitoring Report Prepared for U.S. Army Corps of Engineers, Sacramento District 1325 J Street Sacramento, California 95814 Prepared by Mari-Gold Environmental Consulting Inc. 25385 South Hughes Lane Canby, Oregon 97013 and Novo Aquatic Sciences, Inc. 716 SE Malden Street Portland, Oregon 97202 April 2010 Contents 1 Executive Summary ...................................................................................................................... 1 2 Introduction ................................................................................................................................... 4 3 Methods ...................................................................................................................................... 10 3.1 Sampling Methods Overview ................................................................................................ 10 3.2 Sampling Effort, Timing, and Sampling Locations ................................................................ 10 3.3 Fish Community Sampling .................................................................................................... 14 3.4 Entrainment Sampling .......................................................................................................... 18 3.4.1 Sampling Cells ........................................................................................................... 18 3.4.2 Mobile Entrainment Screen ........................................................................................ 19 3.5 Water Quality Monitoring ...................................................................................................... 22 3.6 Reporting, Data Management, Quality Assurance and Quality Control ................................ 23 3.6.1 Fish Entrainment ........................................................................................................ 23 3.6.2 Fish Community Sampling ......................................................................................... 23 3.6.3 Mortality Estimation .................................................................................................... 23 3.6.4 Data Management ..................................................................................................... 23 4 Results ........................................................................................................................................ 28 4.1 Fish ....................................................................................................................................... 28 4.1.1 Special-status Species ............................................................................................... 30 4.2 Entrainment Monitoring ......................................................................................................... 30 4.2.1 Sacramento River Shipping Channel Locations ......................................................... 34 4.2.2 Stockton Shipping Channel Locations ....................................................................... 34 4.3 Fish Community Monitoring .................................................................................................. 38 4.3.1 Sacramento River Shipping Channel Locations ......................................................... 40 4.3.2 Stockton Shipping Channel Locations ....................................................................... 41 4.4 Fish Length ........................................................................................................................... 55 4.5 Invertebrates ......................................................................................................................... 57 4.6 Bird Activity Observations ..................................................................................................... 60 4.7 Comparison of Monitoring Method Results ........................................................................... 60 4.8 Water Quality Monitoring ...................................................................................................... 63 4.9 Level of Take ........................................................................................................................ 65 4.10 All Years Combined Data ................................................................................................... 68 5 Discussion .................................................................................................................................. 72 5.1 Hypotheses ........................................................................................................................... 72 5.2 Sampling Design Efficiency .................................................................................................. 75 5.3 Overview ............................................................................................................................... 76 5.4 Bird Activity Monitoring ......................................................................................................... 78 5.5 Adaptive Management Strategies ......................................................................................... 78 5.5.1 Entrainment Monitoring .............................................................................................. 79 5.5.2 Fish Community Monitoring ....................................................................................... 79 5.6 Recommendations ................................................................................................................ 79 5.6.1 Entrainment Monitoring .............................................................................................. 79 5.6.2 Fish Community Monitoring ....................................................................................... 80 5.7 Conclusions .......................................................................................................................... 81 6 References ................................................................................................................................. 82 Mari-Gold Environmental Consulting Inc. Page ii Tables Table 1. SRSC & SSC 2009 Maintenance Dredging Locations ............................................................. 11 Table 2. 2009 Entrainment Monitoring Effort at DMP Sites ................................................................... 12 Table 3. 2009 Fish Community Monitoring Effort by Dredging Reach ................................................... 14 Table 4. Ranked List of Fish Encountered from All 2009 Sites from Trawl & Entrainment Monitoring ... 29 Table 5. Ranked List of Fish Encountered From All Sites During 2009 Entrainment Monitoring ........... 31 Table 6. Summary Results of Entrainment Monitoring Events for All SSC Locations ............................ 31 Table 7. Summary Results of Entrainment Events for SRSC Man-made Channel — S-31 DMP Site ... 34 Table 8. Summary Results of Entrainment Events at Light 21 — McCormack Pit DMP Site ................. 35 Table 9. Summary Results of Entrainment Events at Spud Island — Roberts 2 DMP Site ................... 35 Table 10. Summary Results of Entrainment Events at Lower Roberts Island — Roberts 2 DMP Site .. 35 Table 11. Summary Results of Entrainment Events at Windmill Cove — Roberts 2 DMP Site ............. 36 Table 12. Summary Results of Entrainment Events at Upper Roberts Island — Roberts 1 DMP Site .. 36 Table 13. Summary Results of Entrainment Events at Rough & Ready Island —Roberts 1 DMP Site . 36 Table 14. Summary Results of Entrainment Events at Upper Turning Basin — Roberts 1 DMP Site ... 37 Table 15. Extrapolated Fish Entrainment Catch for 2009 by Event Location & Fish Species ................ 37 Table 16. Ranked Catch of Fish from All Sites during 2009 Trawl Monitoring Surveys ......................... 40 Table 17. Summary Catch & Effort Data for Fish Encountered in 2009 Trawl Monitoring Surveys ...... 40 Table 18. Ranked Fish Catch from 2009 Trawl Surveys in SRSC Man-made Channel – S-31 DMP Site ................................................................................................................................... 41 Table 19. Ranked Fish Catch from 2009 Trawl Surveys in All SSC Sites ............................................. 43 Table 20. Summary Results of Trawl Surveys at Scour Pond/ Antioch — Scour Hole DMP Site .......... 45 Table 21. Summary Results of Trawl Surveys at Light 21 — McCormack Pit DMP Site ....................... 45 Table 22. Summary Results of Trawl Surveys at Spud Island — Roberts 2 DMP Site .......................... 48 Table 23. Summary Results of Trawl Surveys at Lower Roberts Island — Roberts 2 DMP Site ........... 48 Table 24. Summary Results of Trawl Surveys at Windmill Cove — Roberts 2 DMP Site ...................... 51 Table 25. Summary Results of Trawl Surveys at Upper Roberts Island — Roberts 1 DMP Site ........... 51 Table 26. Summary Results of Trawl Surveys at Rough & Ready Island — Roberts 1 DMP Site ......... 55 Table 27. Summary Results of Trawl Surveys at Upper Turning Basin — Roberts 1 DMP Site ............ 55 Table 28. Summary Size Statistics for Fish Encountered during 2009 Trawl Surveys .......................... 56 Table 29. Summary Size Statistics for Fish Encountered during 2009 Entrainment Screen Events ...... 57 Table 30. Ranked List for Invertebrates Encountered during 2009 Entrainment Monitoring