Synthesis of Studies in the Fall Low-Salinity Zone of the San Francisco Estuary, September–December 2011

U.S. Geological Survey (USGS) | July 14th, 2014

In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecolo

In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecological Program to explore hypotheses about the ecological role of low-salinity habitat in the San Francisco Estuary—specifically, hypotheses about the importance of fall low-salinity habitat to the biology of delta smelt Hypomesus transpacificus, a species endemic to the San Francisco Estuary and listed as threatened or endangered under federal and state endangered species legislation. The Interagency Ecological Program is a consortium of 10 agencies that work together to develop a better understanding of the ecology of the Estuary and the effects of the State Water Project and Federal Central Valley Project operations on the physical, chemical, and biological conditions of the San Francisco Estuary. The fall low-salinity habitat investigation constitutes one of the actions stipulated in the Reasonable and Prudent Alternative issued with the 2008 Biological Opinion of the U.S. Fish and Wildlife Service, which called for adaptive management of fall Sacramento-San Joaquin Delta outflow following “wet” and “above normal” water years to alleviate jeopardy to delta smelt and adverse modification of delta smelt critical habitat. The basic hypothesis of the adaptive management of fall low-salinity habitat is that greater outflows move the low-salinity zone (salinity 1–6), an important component of delta smelt habitat, westward and that moving the low-salinity zone westward of its position in the fall of recent years will benefit delta smelt, although the specific mechanisms providing such benefit are uncertain. An adaptive management plan was prepared to guide implementation of the adaptive management of fall low-salinity habitat and to reduce uncertainty. This report has three major objectives: •To provide a summary of the results from the first year of coordinated fall low-salinity habitat studies and monitoring. •To provide a synthesis of the results of the fall low-salinity habitat studies and other ongoing research and monitoring, to determine if the available information supports the hypotheses behind the adaptive management of fall low-salinity habitat as set forth in the adaptive management plan. •To begin to put the results from the fall low-salinity habitat studies into context within the larger body of knowledge regarding the San Francisco Estuary and, in particular, the upper San Francisco Estuary, including the Sacramento-San Joaquin Delta, Suisun Bay, and associated embayments.

Synthesizing Relationships Between Winter-Run Chinook Salmon Out-Migration Survival and Water Operations in the Sacramento–San Joaquin Delta

University of California, Davis (UC Davis) | December 19th, 2025

Sacramento River winter-run Chinook Salmon (Oncorhynchus tshawytscha) are an endangered population that faces numerous challenges across its life cycle, including juvenil

Sacramento River winter-run Chinook Salmon (Oncorhynchus tshawytscha) are an endangered population that faces numerous challenges across its life cycle, including juvenile out-migration through the heavily anthropogenically modified Sacramento–San Joaquin Delta, or Delta. Water exports from pumping facilities in the Delta can alter local hydrology and influence movement of out-migrating juveniles, some of which are observed in or near pumping facilities. Monitoring and regulations, intended to protect out-migrating fish through restrictions on pumping, are predicated on assumed relationships among fish observations, water operations, and through-Delta migratory survival. In this study, we use a new conceptual model to review the current state of science for winter-run Chinook Salmon out-migration survival in the Delta, and use simulation modeling to address pertinent knowledge gaps. Results of this study highlight varying support for the influence of Sacramento River flow, temperature, and water exports on routing and survival in different regions of the Delta. The contributions of specific routing pathways to the interior Delta (e.g., through Threemile Slough) to survival, and the relationship between fish entrainment at pumping facilities and overall migratory survival, remain uncertain. Recommended future work includes continued fine-scale acoustic telemetry studies throughout the Delta, novel integrated modeling of monitoring data, and contextualizing the relevance of Delta-based survival to population viability by incorporating explicit uncertainties about survival into existing life-cycle models.

System Reoperation Study, Phase 1: Plan of Study

California Department of Water Resources (DWR) | June 16th, 2011

System reoperation is generally defined as changing the operational and management procedures of existing water system facilities to obtain water resources related benefi

System reoperation is generally defined as changing the operational and management procedures of existing water system facilities to obtain water resources related benefits. Reoperation is considered an alternative to constructing major new facilities, although it may consist of physical modification of existing facilities. The specifics associated with a system reoperation strategy will vary among water purveyors depending upon the complexity of their system and their interest in participating in local and or interregional efforts. There may be opportunity to reoperate portions of California’s statewide water system to yield increased water resources related benefits. This opportunity was recently recognized by the State Legislature in Senate Bill X2 1 (SB X2 1) (Perata, 2008 – Water Code Section 83002.5), which mandated and allocated resources for “planning and feasibility studies to identify potential options for the reoperation of the state's flood protection and water supply systems that will optimize the use of existing facilities and groundwater storage capacity.” Specifically, SB X2 1 stipulated that “the studies shall incorporate appropriate climate change strategies and be designed to determine the potential to achieve the following objectives: (I) Integration of flood protection and water supply systems to increase water supply reliability and flood protection, improve water quality, and provide for ecosystem protection and restoration. (II) Reoperation of existing reservoirs, flood facilities, and other water facilities in conjunction with groundwater storage to improve water supply reliability, flood hazard reduction, and ecosystem protection and to reduce groundwater overdraft. (III) Promotion of more effective groundwater management and protection and greater integration of groundwater and surface water resource uses. (IV) Improvement of existing water conveyance systems to increase water supply reliability, improve water quality, expand flood protection, and protect and restore ecosystems. RELATED DOCUMENTS: System Reoperation Study, Phase 2: Strategy Formulation and Refinement System Reoperation Study, Phase 2: Appendix A: Forecast?Based Operations Analysis System Reoperation Study, Phase 2: Appendix B: Tradeoff Analysis System Reoperation Study, Phase 3 Report: Assessment of Reoperation Strategies System Reoperation, Phase 3: Appendix C: State Water Project and Central Valley Project Integrated Operations Analysis System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

System Reoperation Study, Phase 2: Appendix A: Forecast-Based Operations Analysis

California Department of Water Resources (DWR) | January 29th, 2014

The System Reoperation Study (“Reoperation Study”) is investigating changes in operations and other strategies that may result in improved system performance in terms

The System Reoperation Study (“Reoperation Study”) is investigating changes in operations and other strategies that may result in improved system performance in terms of additional water supply, flood hazard reduction, and ecosystem protection and restoration. It is recognized that existing reservoir operations are typically based on meeting all or some of these three objectives. As such, the Reoperation Study focuses on modifications to existing operations and expansion of these benefits. The Reoperation Study team has developed several reoperation components to evaluate at select river/reservoir systems to quantify benefits and improve understanding of the trade-offs involved. MBK Engineers is providing technical, strategic, and coordination support for the Reoperation Study.  An analysis of Forecast-Based Operation (F-BO) is part of that support. The following report summarizes this effort. F-BO can be applied to any reservoir with a traditional water supply and flood control space allocation paradigm. The incorporation of weather forecasts allows for greater flexibility in the management of the reservoir’s space (flood control versus conservation) and inherently increases the opportunities for gaining additional water supply and flood control benefits through its implementation. System reoperation is informed by historical flood patterns and utilizes records of inflow, outflow, and storage in the reservoirs to develop modified rules for flood releases. Changes to historical operations of the reservoirs is expected to reveal potential for additional water supply storage. With improvements to many of the reservoir facilities, such as increased release capacity, operations are no longer required to be as conservative as they once were. By reducing outflow and allowing an increase in water storage, significant improvements in water supply can be achieved. However, care must be taken so that sufficient water can still be evacuated in the event of a significant forecasted flood. RELATED DOCUMENTS: System Reoperation Study, Phase 1: Plan of Study System Reoperation Study, Phase 2: Strategy Formulation and Refinement System Reoperation Study, Phase 2: Appendix A: Forecast?Based Operations Analysis System Reoperation Study, Phase 2: Appendix B: Tradeoff Analysis System Reoperation Study, Phase 3 Report: Assessment of Reoperation Strategies System Reoperation, Phase 3: Appendix C: State Water Project and Central Valley Project Integrated Operations Analysis System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

System Reoperation Study, Phase 2: Appendix B: Tradeoff Analysis

California Department of Water Resources (DWR) | March 3rd, 2014

The System Reoperation Study is designed to identify potential options for the reoperation of the state’s flood control and water supply systems to meet the following o

The System Reoperation Study is designed to identify potential options for the reoperation of the state’s flood control and water supply systems to meet the following objectives: Water supply reliability Flood hazard reduction Ecosystem protection and restoration Reoperation options include integration of flood control and water supply systems, effective conjunctive management, and improvements to existing water conveyance systems. This phase of the analysis focuses on integration of flood control enhancing water supply systems and expanded conjunctive management with existing conveyance systems. An analysis was designed and performed with the goal of identifying potential reoperation options and to improve understanding of existing system constraints. The analysis is referred to as the tradeoff analysis in recognition of the fact that the existing flood control/water supply system is highly integrated and currently operated to meet water supply, flood control, and ecosystem purposes. Current system operations are complex and frequently constrained by flood control and ecosystem requirements and water rights and contracts for the beneficial use of water. Therefore, reoperation options designed to meet one of the three objectives of the System Reoperation Study frequently create tradeoffs with the other objectives. For example, reductions in required reservoir space for flood control may improve water supply reliability but increase risk of flood damage. The tradeoff analysis is a reconnaissance-level study designed to help illustrate how operational changes designed for one purpose can affect other objectives. Because the existing reservoir and conveyance system is highly integrated and constrained, changes in operation for one purpose create tradeoffs with other purposes. A reconnaissance-level study can help identify these tradeoffs, some of which may be unexpected or unintended, and thereby help guide refinement of more promising options. Model simulations performed in the tradeoff analysis are not refined for the purpose of quantifying benefits or impacts, but rather are intended to illustrate how operational changes in one area affect other areas. For example, how Central Valley Project (CVP) operations can affect State Water Project (SWP) operations, and vice versa. RELATED DOCUMENTS: System Reoperation Study, Phase 1: Plan of Study System Reoperation Study, Phase 2: Strategy Formulation and Refinement System Reoperation Study, Phase 2: Appendix A: Forecast?Based Operations Analysis System Reoperation Study, Phase 2: Appendix B: Tradeoff Analysis System Reoperation Study, Phase 3 Report: Assessment of Reoperation Strategies System Reoperation, Phase 3: Appendix C: State Water Project and Central Valley Project Integrated Operations Analysis System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

System Reoperation Study, Phase 2: Strategy Formulation and Refinement

California Department of Water Resources (DWR) | March 3rd, 2014

The California Department of Water Resources (DWR) is conducting a system reoperation study (SRS) in cooperation with other State and federal agencies, local water distri

The California Department of Water Resources (DWR) is conducting a system reoperation study (SRS) in cooperation with other State and federal agencies, local water districts, groundwater managers, and other stakeholders, to identify potential strategies for reoperation of the statewide flood protection and water supply systems. The opportunity to reoperate portions of California’s statewide water system to yield increased water resources-related benefits was recognized by the State Legislature in Senate Bill X2 1 (SB X2 1) (Perata, 2008 – Water Code Section 83002.5). California’s statewide water system is comprised of a multitude of local, state, and federal projects. These projects include facilities such as dams and reservoirs, hydropower plants, canals, and water diversion structures. Many of these facilities were developed in the early to mid-20th century, and were not designed, constructed, or operated as an integrated water supply and flood management system. Over time, operations of the two largest water supply projects, the State Water Project (SWP), operated by DWR and the Central Valley Project (CVP), operated by the U.S. Department of the Interior’s Bureau of Reclamation (Reclamation), have been integrated to a certain degree. California’s water supply and flood management infrastructure is physically interconnected to the extent that it is technically feasible to move water around the system from Trinity County in the north to Imperial County in the south. However, the management of the water system is not as well integrated as it could be. The underlying logic of the SRS is that California can do much more with its existing water infrastructure by taking advantage of the physical interconnections (and enhancing them) while also operating the system in a coordinated manner to optimize the benefits. The current focus of the SRS is the Central Valley because this region has the highest integration of water supply and flood management facilities. Additionally, the greatest potential for ecosystem restoration through infrastructure reoperation is found in the Central Valley because the existing infrastructure has had a profound effect on aquatic ecosystems. RELATED DOCUMENTS: System Reoperation Study, Phase 1: Plan of Study System Reoperation Study, Phase 2: Strategy Formulation and Refinement System Reoperation Study, Phase 2: Appendix A: Forecast?Based Operations Analysis System Reoperation Study, Phase 2: Appendix B: Tradeoff Analysis System Reoperation Study, Phase 3 Report: Assessment of Reoperation Strategies System Reoperation, Phase 3: Appendix C: State Water Project and Central Valley Project Integrated Operations Analysis System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

System Reoperation Study, Phase 3 Report: Assessment of Reoperation Strategies

California Department of Water Resources (DWR) | August 21st, 2017

The California Department of Water Resources (DWR) is conducting a System Reoperation Study (SRS) in cooperation with other State and federal agencies, local water distri

The California Department of Water Resources (DWR) is conducting a System Reoperation Study (SRS) in cooperation with other State and federal agencies, local water districts, groundwater managers, and other stakeholders, to identify potential strategies for reoperation of the statewide flood protection and water supply systems. The opportunity to reoperate portions of California’s statewide water system to yield increased water resources-related benefits was recognized by the State Legislature in Senate Bill X2 1 (SB X2 1) (Perata 2008). In support of the legislative objectives, DWR developed the SRS to identify viable reoperation strategies and understand how integrated management can: • Improve the reliability of municipal and irrigation water supply. • Reduce flood hazards. • Restore and protect ecosystems. • Buffer the hydrologic variations expected from climate change. • Improve water quality. California’s statewide water system is composed of a multitude of local, State, and federal projects. These projects include dams and reservoirs, hydropower plants, canals, and water diversion structures. Many of these facilities were developed in the early to mid-20th century, and were not designed, constructed, or operated as an integrated water supply and flood management system. Over time, operations of the two largest water supply projects, the State Water Project (SWP), operated by DWR, and the Central Valley Project (CVP), operated by the U.S. Department of the Interior’s Bureau of Reclamation (Reclamation), have been integrated to a certain degree. California’s water supply and flood management infrastructure is physically interconnected to the extent that it is technically feasible to move water around the system, from Trinity County in the north to Imperial County in the south. However, the management of the water system is not as well integrated as it could be. The underlying logic of the SRS is that California can do much more with its existing water infrastructure by taking advantage of the physical interconnections (and enhancing them) while also operating the system in a coordinated manner to optimize the benefits. The current focus of the SRS is the Central Valley, because this region has the highest integration of water supply and flood management facilities. Additionally, the greatest potential for ecosystem restoration through infrastructure reoperation is found in the Central Valley, because the existing infrastructure has had a profound effect on aquatic ecosystems. Figure ES-1 shows the location of the Central Valley and the study area for the SRS. Figure 1-1 also shows major features of the CVP and SWP. RELATED DOCUMENTS: System Reoperation Study, Phase 1: Plan of Study System Reoperation Study, Phase 2: Strategy Formulation and Refinement System Reoperation Study, Phase 2: Appendix A: Forecast?Based Operations Analysis System Reoperation Study, Phase 2: Appendix B: Tradeoff Analysis System Reoperation Study, Phase 3 Report: Assessment of Reoperation Strategies System Reoperation, Phase 3: Appendix C: State Water Project and Central Valley Project Integrated Operations Analysis System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

System Reoperation, Phase 3: Appendix C: State Water Project and Central Valley Project Integrated Operations Analysis

California Department of Water Resources (DWR) | August 21st, 2017

The California Department of Water Resources (DWR) is conducting a system reoperation study (SRS) in cooperation with other state and federal agencies, local water distri

The California Department of Water Resources (DWR) is conducting a system reoperation study (SRS) in cooperation with other state and federal agencies, local water districts, groundwater managers, and other stakeholders to identify potential strategies for reoperation of the statewide flood protection and water supply systems. The opportunity to reoperate portions of California’s statewide water system to yield increased water resources–related benefits was recognized by the State Legislature in Senate Bill (SB) X2 1 (Perata, 2008 – Water Code Section 83002.5). In support of the legislative objectives, DWR developed the SRS to identify viable reoperation strategies and understand how integrated management can: • Improve the reliability of municipal and irrigation water supply • Reduce flood hazards • Restore and protect ecosystem function and habitat conditions • Buffer the hydrologic variations expected from climate change • Improve water quality A component of the SRS is to evaluate how operational improvements of the state and federal water Projects in California may increase water supply and enhance ecosystem function and habitat. The Central Valley Project (CVP) generally has more storage and less conveyance flexibility; the opposite is generally true for the State Water Project (SWP). The SWP and CVP are operated by DWR and the U.S. Bureau of Reclamation (Reclamation), respectively. The operation of the two Projects is coordinated in accordance with the 1986 Coordinated Operating Agreement and other agreements. Though the operation is coordinated, the SWP and CVP are operating as two distinct units. They each have different contractual obligations and operating constraints. Operational improvements using strengths and assets of both Projects may result in improved operational efficiency and help achieve goals of the SRS. The purpose of this effort is to assess potential benefits of operating the SWP and CVP as a single, integrated Project. RELATED DOCUMENTS: System Reoperation Study, Phase 1: Plan of Study System Reoperation Study, Phase 2: Strategy Formulation and Refinement System Reoperation Study, Phase 2: Appendix A: Forecast?Based Operations Analysis System Reoperation Study, Phase 2: Appendix B: Tradeoff Analysis System Reoperation Study, Phase 3 Report: Assessment of Reoperation Strategies System Reoperation, Phase 3: Appendix C: State Water Project and Central Valley Project Integrated Operations Analysis System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

Systematic Screening of Dams for Environmental Flow Assessment and Implementation

Oxford University Press (OUP) | November 30th, 2014

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

California State Water Resources Control Board (SWRCB) | February 15th, 2012

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wild

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wildlife beneficial uses, water quality objectives for the protection of southern delta agricultural beneficial uses, and the program of implementation for those objectives contained in the 2006 Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (2006 Bay- Delta Plan). Figure 1.1 displays the project area corresponding to SJR flow objectives and program of implementation and Figure 1.2 displays the project area for the southern Delta water quality objectives and program of implementation. The information and analytical tools described in this report (referred to hereafter as Draft Technical Report or Technical Report) are intended to provide the State Water Board with the scientific information and tools needed to consider potential changes to these objectives and their associated program of implementation. In this quasi-legislative process, State Water Board staff will propose amendments to the SJR flow objectives for the protection of fish and wildlife beneficial uses, southern Delta water quality objectives for the protection of agricultural beneficial uses, and the program of implementation contained in the 2006 Bay-Delta Plan. Also, the environmental impacts of these amendments will be evaluated in a Substitute Environmental Document (SED) in compliance with the California Environmental Quality Act. Any changes to water rights consistent with the revised program of implementation will be considered in a subsequent adjudicative proceeding.