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Sacramento and Stockton Deepwater Ship Channel Maintenance

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Sacramento and Stockton Deepwater Ship Channel Maintenance Stockton and Sacramento Deepwater Ship Channel Maintenance Dredging Project 2008 Fish Community and Entrainment Monitoring Report Prepared for U.S. Army Corps of Engineers, Sacramento District 1325 J Street Sacramento, California 95814 Prepared by SWCA Environmental Consultants 434 NW 6th Avenue, Suite 304 Portland, Oregon 97209-3600 SWCA 14451 April 2009 Contents Acknowledgements.............................................................................................................................. v Abbreviations...................................................................................................................................... vi 1 Executive Summary.............................................................................................................................1 2 Introduction..........................................................................................................................................3 3 Materials and Methods.........................................................................................................................7 3.1 Sampling Methods Overview........................................................................................................7 3.2 Sampling Effort, Timing, and Sampling Locations........................................................................8 3.3 Fish Community Sampling .........................................................................................................10 3.4 Entrainment Sampling................................................................................................................12 3.4.1 Sampling Cells..........................................................................................................12 3.5 Water Quality Monitoring............................................................................................................14 3.6 Data Analysis, Reporting, Quality Assurance, and Quality Control ............................................14 3.6.1 Fish Entrainment.......................................................................................................14 3.6.2 Fish Community Sampling........................................................................................15 3.6.3 Mortality Estimation...................................................................................................15 3.6.4 Reporting ..................................................................................................................15 3.6.5 Data Management ....................................................................................................15 4 Results...............................................................................................................................................17 4.1 Fish ............................................................................................................................................17 4.1.1 Special-status Species..............................................................................................19 4.2 Entrainment Monitoring ..............................................................................................................19 4.3 Fish Community Monitoring........................................................................................................22 4.3.1 Stockton Shipping Channel (SSC) – San Joaquin River...........................................23 4.3.2 McCormick Pit / Light 19 Reach (SSC):....................................................................25 4.3.3 Sacramento River Shipping Channel (SRSC)...........................................................26 4.3.4 Larval / Post-larval Fish Collection............................................................................28 4.4 Fish Length ................................................................................................................................28 4.5 Invertebrates ..............................................................................................................................30 4.6 Comparison of Monitoring Method Results ................................................................................32 4.7 Water Quality Monitoring............................................................................................................33 4.8 Level of Take..............................................................................................................................33 4.9 Sampling Mortality......................................................................................................................35 4.10 Vouchered Specimens ...............................................................................................................37 4.11 Sampling Design Efficiency........................................................................................................37 4.11.1 Species Richness .....................................................................................................38 4.11.2 Catch per Unit Effort .................................................................................................38 4.12 Statistical Analysis of Fish Size..................................................................................................39 4.12.1 Channel Catfish ........................................................................................................39 4.12.2 White Catfish ............................................................................................................39 4.12.3 Special-status Length Data.......................................................................................40 4.12.4 Demersal and Non-demersal Fish ............................................................................40 5 Discussion .........................................................................................................................................41 5.1 Hypotheses ................................................................................................................................41 SWCA Environmental Consultants SWCA 14451 Page i 5.1.1 Sampling Design Efficiency ......................................................................................43 5.1.2 Statistical Analysis ....................................................................................................44 5.2 Overview ....................................................................................................................................45 5.3 Discussion of Entrainment Monitoring........................................................................................47 5.3.1 Entrainment Screen ..................................................................................................47 5.3.2 Entrainment Cells......................................................................................................48 5.4 Discussion of Fish Community Monitoring .................................................................................48 5.5 Inter-annual Variation.................................................................................................................49 5.5.1 Bird Activity Monitoring .............................................................................................50 5.5.2 Survival of Entrained Fish.........................................................................................50 6 Adaptive Management.......................................................................................................................51 6.1 Entrainment Monitoring ..............................................................................................................51 6.2 Fish Community Monitoring........................................................................................................52 7 Recommendations.............................................................................................................................53 7.1 Entrainment Monitoring ..............................................................................................................53 7.2 Fish Community Monitoring........................................................................................................54 8 Conclusions .......................................................................................................................................55 9 References ........................................................................................................................................56 Figures 1. Project area map, dredge reaches, and DMP Sites 2. S-31 – Man-made Channel 3. Sandy Beach – Rio Vista 4. Decker Island – Natural Channel 5. Scour Pond – Lower – Antioch/West Island 6. Scour Pond – Upper – Antioch/West Island 7. McCormick Pit – Light 19 8. Bradford Island 9. Roberts – Port of Stockton 10. Roberts – Sediment Trap 11. Otter trawl diagram 12. Fish community sampling 13. Entrainment sampling cell at Decker Island DMP site 14. Discharge pipeline splitter valve at Roberts Island DMP 15. Mobile entrainment collection screen system 16. Mobile entrainment screen at Roberts Island DMP 17. Mobile entrainment screen at Roberts Island DMP 18. Two types of screen used for entrainment sampling in 2008 19. Water quality monitoring during fish community sampling 20. Specimens collected during fish community sampling 21. Specimens collected during entrainment sampling 22. Percent native fish collected at each fish community monitoring location
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