Stockton and Sacramento Deep Water Ship Channel Maintenance Dredging and Dredge Material Placement Projects 2012 Fish Community, Entrainment and Water Quality 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 March 2013 Contents 1 Executive Summary .................................................................................................................. 1 2 Introduction ............................................................................................................................... 4 3 Methods .................................................................................................................................... 9 3.1 Monitoring Methods Overview ....................................................................................... 9 3.2 Monitoring Effort, Timing, and Locations ...................................................................... 10 3.3 Entrainment Monitoring ................................................................................................ 13 3.3.1 Mobile Entrainment Screen ............................................................................... 13 3.4 Fish Community Monitoring ......................................................................................... 19 3.5 Water Quality Monitoring ............................................................................................. 24 3.6 Reporting, Data Management, Quality Assurance and Quality Control ....................... 25 3.6.1 Entrainment Monitoring ..................................................................................... 25 3.6.2 Fish Community Monitoring .............................................................................. 25 3.6.3 Mortality Estimation .......................................................................................... 25 3.6.4 Data Management ............................................................................................ 26 3.6.5 Quality Assurance and Quality Control ............................................................. 26 4 Results ................................................................................................................................... 28 4.1 Fish .............................................................................................................................. 28 4.1.1 Special-status Species ...................................................................................... 30 4.2 Entrainment Monitoring ................................................................................................ 31 4.2.1 Stockton Deep Water Shipping Channel Locations .......................................... 32 4.3 Fish Community Monitoring ......................................................................................... 35 4.3.1 Stockton Deep Water Shipping Channel Locations .......................................... 38 4.4 Fish Length .................................................................................................................. 44 4.4.1 Entrainment Monitoring ..................................................................................... 44 4.5 Invertebrates ................................................................................................................ 48 4.6 Bird and Marine Mammal Activity Observations .......................................................... 50 4.7 Comparison of Monitoring Method Results .................................................................. 51 4.8 Water Quality Monitoring ............................................................................................. 54 4.9 Level of Take ................................................................................................................ 55 4.10 Monitoring Mortality ..................................................................................................... 57 4.11 Vouchered Specimens ................................................................................................. 58 4.12 Combined Data for All Years ........................................................................................ 59 5 Discussion .............................................................................................................................. 65 5.1 Hypotheses .................................................................................................................. 65 5.2 Monitoring Design Efficiency ....................................................................................... 70 5.3 Overview ...................................................................................................................... 71 5.4 Bird Activity Monitoring ................................................................................................ 74 5.5 Adaptive Management Strategies and Recommendations for Future Monitoring Efforts .. 75 5.5.1 Entrainment Monitoring ..................................................................................... 75 5.5.2 Fish Community Monitoring .............................................................................. 77 5.6 Conclusions ................................................................................................................. 78 6 References ............................................................................................................................. 79 Appendix A. Special Status Species Life History Information .........................................................A-1 Appendix B. Water Quality Data .....................................................................................................B-1 Appendix C. Field Data Collection Forms and Database ................................................................C-1 Mari-Gold Environmental Consulting, Inc. & Novo Aquatic Sciences, Inc. - 2012 Fish Monitoring Report Page i List of Tables Table 1. 2012 maintenance dredge reaches — Roberts 1 DMP ...........................................................................11 Table 2. 2012 entrainment monitoring effort by dredge reach — Roberts 1 DMP ............................................... 12 Table 3. 2012 fish community monitoring effort by dredge reach — Roberts 1 DMP .......................................... 12 Table 4. Ranked list of fish encountered at all 2012 sites during fish community and entrainment monitoring ... 28 Table 5. Ranked list of fish encountered from all sites during 2012 entrainment monitoring ............................... 31 Table 6a. Summary data for fish encountered during entrainment monitoring at Rough and Ready Island DR – Roberts 1 DMP .................................................................................... 32 Table 6b. Summary data for fish encountered during entrainment monitoring at Ore Dock DR – Roberts 1 DMP ............................................................................................................ 33 Table 6c. Summary data for fish encountered during entrainment monitoring at Upper Roberts DR – Roberts 1 DMP .................................................................................................... 33 Table 7. Extrapolated results from all 2012 fish entrainment monitoring .............................................................. 34 Table 8. Ranked list of fish encountered at all sites during 2012 fish community monitoring .............................. 35 Table 9. Summary catch and effort data for all fish encountered during 2012 fish community monitoring .......... 37 Table 10a. Summary data for fish encountered during fish community monitoring at Rough and Ready Island DR – Roberts 1 DMP ................................................................................. 38 Table 10b. Summary data for fish encountered during fish community monitoring at Ore Dock DR – Roberts 1 DMP .......................................................................................................... 40 Table 10c. Summary data for fish encountered during fish community monitoring at Upper Roberts DR – Roberts 1 DMP .................................................................................................. 42 Table 11. Summary length data for fish encountered during all 2012 entrainment monitoring ............................ 44 Table 12. Summary length data for fish encountered during all 2012 fish community monitoring ....................... 46 Table 13. Summary data for invertebrates encountered during all 2012 entrainment monitoring ....................... 48 Table 14. Summary data for invertebrates encountered in all 2012 fish community monitoring .......................... 49 Table 15. Extrapolated total of invertebrates entrained during 2012 by dredge reach — Roberts 1 DMP .......... 49 Table 16. Demersal fish encountered during fish community and entrainment monitoring at each 2012 dredge reach ....................................................................................................................... 51 Table 17. Comparison of relative abundance of encountered fish species by monitoring method ...................... 53 Table 18. ESA and CESA incidental take allotments for ship channel fish monitoring ......................................... 55 Table 19. Total estimated fish mortality among fish observed during 2012 entrainment