San Francisco Bay/Sacramento-San Joaquin Delta Estuary (Bay-Delta) Program

Draft Technical Report on the Scientific Basis for Alternative San Joaquin River Flow and Southern Delta Salinity Objectives.

Supporting Information

The following information is provided to assist with public review of the Draft Technical Report on the Scientific Basis for Alternative San Joaquin River Flow and Southern Delta Salinity Objectives (see Technical Report) dated October 29, 2010.

Spreadsheet Demonstrating Water Supply Impact Analysis Methodology (by SWRCB staff)
Spreadsheet of Flow Data Used for Hydrologic Analysis (by SWRCB staff)
Sources of Salinity Data for Regression Analysis

Key References in Technical Report
Anadromous Fish Restoration Program (AFRP). 1995. Working Paper on Restoration Needs: Habitat Restoration Actions to Double Natural Production of Anadromous Fish in the Central Valley of California. Volume 3. Prepared for the U.S. Fish and Wildlife Services under the direction of the Anadromous Fish Restoration Program Core Group. Stockton, CA.
Anadromous Fish Restoration Program (AFRP). 2005. Recommended streamflow schedules to meet the AFRP doubling goal in the San Joaquin River Basin. 27 September 2005.
Baker, P.F., and Morhardt., J.E. 2001. Survival of Chinook Salmon Smolts in the Sacramento-San Joaquin Delta and Pacific Ocean. Contributions to the Biology of Central Valley Salmonids 2: 163-182.
Bowen, M.D., Hiebert, S., Hueth, C., and Maisonneuve, V. 2009. 2009 Effectiveness of a Non-Physical Fish Barrier at the Divergence of the Old and San Joaquin Rivers (CA). U.S. Department of the Interior Technical Memorandum 86-68290-09-05.
Brandes, P.L. and McLain, J.S. 2001. Juvenile Chinook salmon abundance, distribution, and survival in the Sacramento-San Joaquin Estuary. In: R.L. Brown, editor, Contributions to the biology of Central Valley salmonids. Volume 2. California Department of Fish and Game Fish Bulletin 179:39-136.
Brown, L.R., and Bauer, M.L. 2009. Effects of Hydrologic Infrastructure on Flow Regimes of California's Central Valley Rivers: Implications for Fish Populations. River Research and Applications. DOI: 10.1002/rra.1293.
Bunn, S.E. and Arthington, A.H. 2002. Basic Principles and Ecological Consequences of Altered Flow Regimes for Aquatic Biodiversity. Environmental Management 30(4):492-507.
Cain, J.R., Walkling, R.P., Beamish, S., Cheng, E., Cutter, E., and Wickland, M. 2003. San Joaquin Basin Ecological Flow Analysis. National Heritage Institute. 247 pages.
California Department of Fish and Game (DFG). 2005a. California Department of Fish and Game Supplemental Comments and Recommendations on the Vernalis Flow and Salmon Doubling Objectives in the 1995 Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin River Delta Estuary.
California Department of Fish and Game (DFG). 2005b. San Joaquin River Fall-Run Chinook Salmon Population Model. Report to the State Water Resources Control Board.
California Department of Fish and Game (DFG). 2009. San Joaquin River Fall-run Chinook Salmon Population Model Version 1.6. Report to the State Water Resources Control Board.
California Department of Fish and Game (DFG). 2010a. California Department of Fish and Game Flows Needed in the Delta to Restore Anadromous Salmonid Passage from the San Joaquin River at Vernalis to Chipps Island.
California Department of Fish and Game (DFG). 2010b. Effects of Water Temperature on Anadromous Salmonids in the San Joaquin River Basin.
California Department of Water Resources (DWR). 2007a. California Central Valley Unimpaired Flow Data, Fourth Edition, Draft. May 2007.
California Department of Water Resources (DWR). 2007b. Comments on SWRCB Southern Delta Salinity Standards Modeling Requests (Tara Smith, Parviz Nader-Tehrani, Erik Reyes, Mark Holderman). May 2007.
Central Valley Regional Water Quality Control Board (CVRWQCB). 2007. City of Tracy Wastewater Treatment Plan NPDES Permit., Attachments F & H (CVRWQCB Order R5-2007-0036). May 2007.
Fleenor, W., Bennett, W., Moyle, P.B., and Lund, J. 2010. On developing prescriptions for freshwater flows to sustain desirable fishes in the Sacramento-San Joaquin Delta. Submitted to the State Water Resources Control Board regarding flow criteria for the Delta necessary to protect public trust resources. 43 pages.
Florida Administrative Code. Rule 40D-8.041. Effective July 12, 2010.
Freeman, M.C., Bowen, Z.H., Bovee, K.D., and Irwin, E.R. 2001. Flow and Habitat Effects on Juvenile Fish Abundance in Natural and Altered Flow Regimes. Ecological Applications 11(1).
Freyer, F., and Healey, M.P. 2003. Fish Community Structure and Environmental Correlates in the Highly Altered Southern Sacramento-San Joaquin Delta. Environmental Biology of Fishes 66: 123-132.
Hankin, D., Dauble, D., Pizzimentieti, J.J., Smith, P. 2010. The Vernalis Adaptive Management Program (VAMP): Report of the 2010 Review Panel. May 2010.
Holbrook, C.M., Perry, R.W., and Adams, N.S. 2009. Distribution and Joint Fish-Tag Survival of Juvenile Chinook Salmon Migrating Through the Sacramento-San Joaquin River Delta, 2008. Geological Survey Open File Report 2009-1204. 30 pages.
Jeffres, C.A., Opperman, J.J., and Moyle, P.B. 2008. Ephemeral Floodplain Habitats Provide Best Growth Conditions for Juvenile Chinook Salmon in a California River. Environmental Biology of Fishes 83: 449-458.
Junk, W.J., Bayley, P.B., and Sparks, R.E. 1989. The flood pulse concept in river-floodplain systems. Special publication. Canadian Journal of Fisheries and Aquatic Science 106:110–127.
Kimmerer, W. and M. Nobriga. 2008. Investigating particle transport and fate in the Sacramento-San Joaquin Delta using a Particle Tracking Model. San Francisco Estuary and Watershed Science 6(1):Article 4.
Kjelson, M.A., Raquel, P.F., and Fisher, F.W. 1981. Influences of freshwater inflow on Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento-San Joaquin Estuary. In P.D. Cross and D.L. Williams, editors, Proceedings of the National Symposium on Freshwater Inflow to Estuaries, pp. 88-108. U.S. Fish and Wildlife Service, FWS/OBS- 81-04.
Kjelson, M.A. and Brandes, P.L., 1989. The use of smolt survival estimated to quantify the effects of habitat changes on salmonid stocks in the Sacramento-San Joaquin River, CA. Canadian Special Publication of Fisheries Aquatic Science 105: 100-115.
Lindley, S.T., Grimes, C.B., Mohr, M.S., Peterson, W., Stein, J., Anderson, J.T., Botsford, L.W., Buttom, D.L., Busack, C.A., Collier, T.K., Ferguson, J., Garza, J.C., Grover, A.M. Hankin, D.G., Kope, R.G., Lawson, P.W., Low, A., MacFarlane, R.B., Moore, K., Palmer-Zwahlen, M., Schwing, F.B., Smith, J., Tracy, C., Webb, R., Wells, B.K., Williams, T.H. 2009. What Caused the Sacramento River Fall Chinook Stock Collapse? Pacific Fishery Management Council. March 18, 2009.
Lytle, D.A., and Poff, N.L. 2004. Adaptation to Natural Flow Regimes. Trends in Ecology and Evolution 19: 94-100.
Marchetti, M.P., and Moyle, P.B. 2001. Effects of Flow Regime on Fish Assemblages in a Regulated California Stream. Ecological Applications 11: 530-539.
Mazvimavi, D., Madamombe, E. and Makurira, H. 2007. Assessment of Environmental Flow Requirements for River Basin Planning in Zimbabwe. Physics and Chemistry of the Earth 32: 995-1006.
McBain and Trush, Inc. editor. 2002. San Joaquin River Restoration Study Background Report. Prepared for Friant Water Users Authority. Lindsay, California and Natural Resources Defense Council, San Francisco California. Arcata, California. December 2002.
McElhany, P., Ruckelshaus, M., Ford, M.J., Wainwright, T.C., and Bjorkstedt, E.P. 2000. Viable salmonid populations and the recovery of evolutionarily significant units. U.S. Dept. of Commerce. NOAA Tech. Memo. NMFS-NWFSC-42,156 pp.
Mesick, C.F. 2001. Unpublished. Factors that Potentially Limit the Populations of Fall-Run Chinook Salmon in the San Joaquin River Tributaries.
Mesick, C.F., and Marston, D. 2007. Provisional Draft: Relationships Between Fall-Run Chinook Salmon Recruitment to the Major San Joaquin River Tributaries and Stream Flow, Delta Exports, the Head of the Old River Barrier, and Tributary Restoration Projects from the Early 1980s to 2003.
Mesick, C.F., McLain, J.S., Marston, D., and Heyne, T. 2008. Limiting Factor Analyses & Recommended Studies for Fall-Run Chinook Salmon and Rainbow Trout in the Tuolumne River. California Department of Fish and Game. Prepared for the U. S. Fish and Wildlife Service. Draft Report.
Mesick, C. 2009. The high risk of extinction for the natural Fall-Run Chinook salmon population in the lower Tuolumne River due to insufficient instream flow releases. U.S. Fish and Wildlife Service, Energy and Instream Flow Branch, Sacramento, CA. 4 September 2009. Exhibit No. FWS-50.
Mesick, C.F. 2010. Relationships between Flow, Water Temperature, and Exports in the San Joaquin River Delta and the Rate that Adult Merced River Hatchery Fall-Run Chinook Salmon with Coded-Wire-Tags Were Recovered in the Central Valley Escapement and the Ocean Fisheries.
Moyle, P.B., and Mount, J.F. 2007. Homogenous Rivers, Homogenous Faunas. Proceedings of the National Academy of Science. 104: 5711-5712.
National Marine Fisheries Service (NMFS). 2009a. Endangered Species Act Section 7 Consultation. Biological Opinion and Conference Opinion on the Long-Term Operations of the Central Valley Project and State Water Project. June 2009.
National Marine Fisheries Service (NMFS). 2009b. Endangered Species Act Section 7 Consultation. Biological Opinion and Conference Opinion on the Long-Term Operations of the Central Valley Project and State Water Project, Appendix 5. June 2009.
Newman, K.B. 2008. An Evaluation of Four Sacramento-San Joaquin River Delta Juvenile Salmon Survival Studies. 181 pages.
Petts, G.E. 2009. Instream-Flow Science for Sustainable River Management. Journal of the American Water Resources Association 45: 1071-1086.
Poff, N.L.. Allan, J.K., Bain, M.B., Karr, J.R., Prestegaard, K.L., Richter, B.D., Sparks, R.E., and Stromberg, J.C. 1997. The Natural Flow Regime. Bioscience 47: 769-784.
Poff, N.L.. Olden, J.D., Merritt, D.M., and Pepin, D.M. 2007. Homogenization of Regional River Dynamics by Dams and Global Biodiversity Implications. Proceedings of the National Academy of Sciences 104: 5732-5737.
Rosenfield, J., Swanson, C., Cain, J., and Cox, C. 2010. Testimony of Dr. Jonathan Rosenfield, Dr. Christina Swanson, John Cain, and Carson Cox regarding Flow Criteria for the Delta Necessary to Protect Public Trust Resources: General Analytical Framework.
San Joaquin River Group Authority (SJRGA). 2007. 2006 Annual Technical Report: On implementation and monitoring of the San Joaquin River Agreement and the Vernalis Adaptive Management Plan. 136 pages.
San Joaquin River Group Authority (SJRGA). 2008. 2007 Annual Technical Report: On implementation and monitoring of the San Joaquin River Agreement and the Vernalis Adaptive Management Plan. 128 pages.
San Joaquin River Group Authority (SJRGA). 2009. 2008 Annual Technical Report: On implementation and monitoring of the San Joaquin River Agreement and the Vernalis Adaptive Management Plan. 128 pages.
San Joaquin River Group Authority (SJRGA). 2010. 2009 Annual Technical Report: On implementation and monitoring of the San Joaquin River Agreement and the Vernalis Adaptive Management Plan. 128 pages.
San Joaquin River Technical Committee (SJRTC). 2008. Summary Report of the Vernalis Adaptive Management Plan for 2000-2008. Report prepared for the Advisory Panel Review conducted by the Delta Science Program, December 22, 2008, 84 pages.
Sparks, R.E. 1995. Need for Ecosystem Management of Large Rivers and Their Floodplains. Bioscience 45: 168-182.
State Water Resources Control Board (State Water Board). 2000. Revised Water Right Decision 1641 in the Matter of Implementation of Water Quality Objectives for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary.
State Water Resources Control Board (State Water Board). 2010, Development of Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem. August 3, 2010.
The Bay Institute (TBI) and Natural Resources Defense Council (NRDC). 2010a. Exhibit 1 - Written Testimony of Jonathan Rosenfield, Ph.D., Christina Swanson, Ph.D., John Cain, and Carson Cox Regarding General Analytical Framework.
The Bay Institute (TBI) and Natural Resources Defense Council (NRDC). 2010b. Exhibit 3 - Written Testimony of Christina Swanson, Ph.D., John Cain, Jeff Opperman, Ph.D., and Mark Tompkins, Ph.D. Regarding Delta Inflows.
U.S. Army Corps of Engineers (USACE). 2002. Sacramento and San Joaquin River Basins Comprehensive Study. December 2002. Sacramento District.
U.S. Department of the Interior (DOI). 2010. Comments regarding the California State Water Resources Control Board notice of public informational proceeding to develop Delta flow criteria for the Delta ecosystem necessary to protect public trust resources (Exhibit 1).
U.S. Fish and Wildlife Service (USFWS). 1987. Exhibit 31: The Needs of Chinook Salmon, Oncorhyncus tshawytscha, in the Sacramento-San Joaquin Estuary. Entered by the U.S. Fish and Wildlife Service for the State Water Resources Control Board, 1987 Water Quality/Water Rights Proceeding on the San Francisco Bay / Sacramento-San Joaquin Delta.
Vogel, D. 2010. Evaluation of Acoustic-Tagged Juvenile Chinook Salmon Movements in the Sacramento-San Joaquin Delta during the 2009 Vernalis Adaptive Management Program. March 2010. Natural Resource Scientists, Inc. Red Bluff, CA.

Questions or Comments about the San Joaquin River Flow and Southern Delta Salinity Objectives?

Please contact:

Diane Riddle, Division of Water Rights, (916) 341- 5297
or
Mark Gowdy, Division of Water Rights, (916) 341-5432