Draft Attachment 1 Assessment of Fisheries Impacts Within the Sacramento- San Joaquin Delta Fisheries and Aquatic Ecosystems Technical Report Shasta Lake Water Resources Investigation Prepared by: United States Department of the Interior Bureau of Reclamation Mid-Pacific Region U.S. Department of the Interior Bureau of Reclamation June 2013 Contents Contents Chapter 1 Environmental Setting ............................................................................................. 1-1 1.1 Historical Factors Affecting the Bay-Delta ..................................................................... 1-3 1.1.1 Delta ..................................................................................................................... 1-3 1.1.2 Suisun Bay ........................................................................................................... 1-3 1.1.3 San Pablo Bay ...................................................................................................... 1-5 1.1.4 San Francisco Bay................................................................................................ 1-5 1.2 Delta Hydrology............................................................................................................... 1-5 1.2.1 History.................................................................................................................. 1-5 1.2.2 Water Project Development ................................................................................. 1-6 1.3 Loss of Wetlands.............................................................................................................. 1-6 1.4 Pollutants.......................................................................................................................... 1-7 1.5 Commercial Fishing ......................................................................................................... 1-7 1.6 Introduced Species ........................................................................................................... 1-8 1.7 Salinity ........................................................................................................................... 1-10 1.8 Dredging ........................................................................................................................ 1-10 1.9 Flood Control Operations .............................................................................................. 1-11 1.10 Unscreened Diversions .................................................................................................. 1-11 1.11 Tides and Ocean Conditions .......................................................................................... 1-11 1.12 Facilities and Operations of the SWP and CVP Within the Delta ................................. 1-12 1.12.1 SWP Delta Facilities .......................................................................................... 1-12 1.12.2 CVP Facilities .................................................................................................... 1-17 1.13 Other Facilities ............................................................................................................... 1-19 1.14 Fisheries and Aquatic Resources ................................................................................... 1-19 1.14.1 Phytoplankton .................................................................................................... 1-20 1.14.2 Zooplankton ....................................................................................................... 1-21 1.14.3 Benthic and Epibenthic Macroinvertebrates ...................................................... 1-22 1.14.4 Fish ..................................................................................................................... 1-24 Chapter 2 Potential Effects of Project Alternatives on Fish Habitat in the Delta ............... 2-1 2.1 Delta Outflow ................................................................................................................... 2-1 2.2 Delta Inflow ................................................................................................................... 2-11 2.3 Sacramento River Inflow ............................................................................................... 2-20 2.4 San Joaquin River Flow at Vernalis............................................................................... 2-29 2.5 Entrapment Zone Location and X2 ................................................................................ 2-39 2.6 Old and Middle Rivers Reverse Flows........................................................................... 2-49 2.7 SWP and CVP Export Operations ................................................................................. 2-62 2.8 Estimated Fish Entrainment/ Losses .............................................................................. 2-83 Chapter 3 References ................................................................................................................. 3-1 i Draft – June 2013 Shasta Lake Water Resources Investigation Biological Resource Appendix – Fisheries and Aquatic Ecosystems Technical Report Attachment 1-Assessment of Fisheries Impacts Within the Sacramento-San Joaquin Delta Tables Table 1-1. Fish Species Inhabiting the Delta ............................................................................... 1-9 Table 1-2. Status of Fishes of the Sacramento-San Joaquin Delta ............................................ 1-25 Table 1-2. Status of Fishes of the Sacramento-San Joaquin Delta (contd.) .............................. 1-26 Table 2-1. Delta Outflow (cfs) in January, Modeled for Existing Project Alternatives .............. 2-2 Table 2-2. Delta Outflow (cfs) in February, Modeled for Existing Project Alternatives ............ 2-3 Table 2-3. Delta Outflow (cfs) in March, Modeled for Existing Project Alternatives ................ 2-3 Table 2-4. Delta Outflow (cfs) in April, Modeled for Existing Project Alternatives .................. 2-3 Table 2-5. Delta Outflow (cfs) in May, Modeled for Existing Project Alternatives ................... 2-4 Table 2-6. Delta Outflow (cfs) in June, Modeled for Existing Project Alternatives ................... 2-4 Table 2-7. Delta Outflow (cfs) in July, Modeled for Existing Project Alternatives .................... 2-4 Table 2-8. Delta Outflow (cfs) in August, Modeled for Existing Project Alternatives ............... 2-5 Table 2-9. Delta Outflow (cfs) in September, Modeled for Existing Project Alternatives ......... 2-5 Table 2-10. Delta Outflow (cfs) in October, Modeled for Existing Project Alternatives ............ 2-5 Table 2-11. Delta Outflow (cfs) in November, Modeled for Existing Project Alternatives ........ 2-6 Table 2-12. Delta Outflow (cfs) in December, Modeled for Existing Project Alternatives ........ 2-6 Table 2-13. Delta Outflow (cfs) in January, Modeled for Future Project Alternatives ............... 2-6 Table 2-14. Delta Outflow (cfs) in February, Modeled for Future Project Alternatives ............. 2-7 Table 2-15. Delta Outflow (cfs) in March, Modeled for Future Project Alternatives ................. 2-7 Table 2-16. Delta Outflow (cfs) in April, Modeled for Future Project Alternatives ................... 2-7 Table 2-17. Delta Outflow (cfs) in May, Modeled for Future Project Alternatives .................... 2-8 Table 2-18. Delta Outflow (cfs) in June, Modeled for Future Project Alternatives .................... 2-8 Table 2-19. Delta Outflow (cfs) in July, Modeled for Future Project Alternatives ..................... 2-8 Table 2-20. Delta Outflow (cfs) in August, Modeled for Future Project Alternatives ................ 2-9 Table 2-21. Delta Outflow (cfs) in September, Modeled for Future Project Alternatives .......... 2-9 Table 2-22. Delta Outflow (cfs) in October, Modeled for Future Project Alternatives ............... 2-9 Table 2-23. Delta Outflow (cfs) in November, Modeled for Future Project Alternatives ......... 2-10 Table 2-24. Delta Outflow (cfs) in December, Modeled for Future Project Alternatives ......... 2-10 Table 2-25. Delta Inflow (cfs) in January, Modeled for Existing Project Alternatives ............. 2-11 Table 2-26. Delta Inflow (cfs) in February, Modeled for Existing Project Alternatives ........... 2-12 Table 2-27. Delta Inflow (cfs) in March, Modeled for Existing Project Alternatives ............... 2-12 Table 2-28. Delta Inflow (cfs) in April, Modeled for Existing Project Alternatives ................. 2-12 Table 2-29. Delta Inflow (cfs) in May, Modeled for Existing Project Alternatives .................. 2-13 Table 2-30. Delta Inflow (cfs) in June, Modeled for Existing Project Alternatives .................. 2-13 Table 2-31. Delta Inflow (cfs) in July, Modeled for Existing Project Alternatives ................... 2-13 Table 2-32. Delta Inflow (cfs) in August, Modeled for Existing Project Alternatives .............. 2-14 Table 2-33. Delta Inflow (cfs) in September, Modeled for Existing Project Alternatives ........ 2-14 Table 2-34. Delta Inflow (cfs) in October, Modeled for Existing Project Alternatives ............ 2-14 Table 2-35. Delta Inflow (cfs) in November, Modeled for Existing Project Alternatives ........ 2-15 Table 2-36. Delta Inflow (cfs) in December, Modeled for Existing Project Alternatives ......... 2-15 Table 2-37. Delta Inflow (cfs) in January, Modeled for Future Project Alternatives ................ 2-15 ii Draft – June 2013 Contents Table 2-38. Delta Inflow (cfs) in February, Modeled