Recent advances in understanding flow dynamics and transport of water-quality constituents in the Sacramento–San Joaquin River Delta

University of California, Davis (UC Davis) | December 1st, 2016

This chapter describes advances during the past decade in understanding flow dynamics and how water-quality constituents, such as salinity, heat, oxygen, nutrients, conta

This chapter describes advances during the past decade in understanding flow dynamics and how water-quality constituents, such as salinity, heat, oxygen, nutrients, contaminants, and more, move within California’s Sacramento-San Joaquin River Delta. Water-quality constituents are affected by water diversions and other human manipulations of flow and they greatly affect the quantity and quality of habitats in the Delta. Along with human intervention, the Pacific Ocean, the Central Valley watershed, and the atmosphere, are a few drivers of flow and transport in the Delta. These drivers provide a conceptual framework for presenting recent findings. The tremendous expansion of acoustic and optical instruments utilized in the Delta over the past decade has greatly improved our understanding of how tidal variability affects flow and transport. Sediment is increasingly viewed as a diminishing resource needed to sustain habitat and tidal marsh, especially as sea level rises. Connections between the watershed, Delta, and San Francisco Bay that have been studied recently highlight that a landscape view of this system is needed rather than consideration of each region individually. Interactions of multiple drivers and information gaps are discussed.

Recommendations for a Modeling Framework to Answer Nutrient Management Questions in the Sacramento-San Joaquin Delta

San Francisco Estuary Institute (SFEI) | March 1st, 2016

Management actions in the Delta related to nutrients could cost billions of dollars to implement in the coming decades depending on decisions that will come before the Ce

Management actions in the Delta related to nutrients could cost billions of dollars to implement in the coming decades depending on decisions that will come before the Central Valley Regional Water Quality Control Board (Water Board). The complexity of the Delta ecosystem and the range of questions to be addressed demand that numerical, processed-based water quality modeling be part of Delta management efforts. In light of this fact, the Water Board convened the Modeling Science Workgroup in 2015, and tasked it with advising on the development and use of water quality models as one component of the Water Board’s Nutrient Research Plan. The Charge to the Modeling Science Workgroup (included in Appendix B) was to provide advice to the Water Board on:  · The types of models would be needed to answer the nutrient management questions raised by stakeholders,  · Organizational arrangements to support and maximize the benefits of models, and  · Cost estimates for the modeling task and how such work might be phased over time. 

Reconciling fish and farms: Methods for managing California rice fields as salmon habitat

PLOS | February 24th, 2021

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the pa

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California’s Central Valley have emerged as ecologically functioning floodplain rearing habitat for juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods to enhance habitat benefits for fall-run Chinook Salmon reared on winter-flooded rice fields in the Yolo Bypass, a modified floodplain managed for flood control, agriculture, and wildlife habitat in the Sacramento River Valley of California. Investigations included studying the effect of 1) post-harvest field substrate; 2) depth refugia; 3) duration of field drainage; and 4) duration of rearing occupancy on in-situ diet, growth and survival of juvenile salmon. Post-harvest substrate treatment had only a small effect on the lower trophic food web and an insignificant effect on growth rates or survival of rearing hatchery-origin, fall-run Chinook Salmon. Similarly, depth refugia, created by trenches dug to various depths, also had an insignificant effect on survival. Rapid field drainage yielded significantly higher survival compared to drainage methods drawn out over longer periods. A mortality of approximately one third was observed in the first week after fish were released in the floodplain. This initial mortality event was followed by high, stable survival rates for the remainder of the 6-week duration of floodplain rearing study. Across years, in-field survival ranged 7.4–61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California’s recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant than those sampled concurrently in the adjacent Sacramento River channel. Correspondingly, observed somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater than concurrently and previously observed growth rates in the adjacent Sacramento River. The abundance of food resources and exceptionally high growth rates observed.

Record of Decision, Trump Administration Action 5 Operations Plan for the Central Valley and State Water Projects, per Executive Order 14181

U.S. Bureau of Reclamation (USBR) | December 4th, 2025

On January 24, 2025, President Donald J. Trump issued Executive Order 14181 “Emergency Measures To Provide Water Resources In California And Improve Disaster Response I

On January 24, 2025, President Donald J. Trump issued Executive Order 14181 “Emergency Measures To Provide Water Resources In California And Improve Disaster Response In Certain Areas.” A Presidential Memorandum titled “Putting People Over Fish” was signed four days before the Executive Order and references a reliable water supply, but the specific direction to the CVP is found in Executive Order 14181. Section 2 of Executive Order 14181 requires, among other measures, (c) The Secretary of the Interior, including through the Bureau of Reclamation, shall utilize his discretion to operate the CVP to deliver more water and produce additional hydropower, including by increasing storage and conveyance, and jointly operating federal and state facilities, to high­need communities, notwithstanding any contrary State or local laws. The Bureau of Reclamation shall take all available measures to ensure that State agencies — including the California Department of Water Resources — do not interfere with the Bureau of Reclamation’s operation of the project to maximize water delivery to high­need communities or otherwise, including but not limited to the issuance of a new Record of Decision maximizing water deliveries and consistent with the 2020 Record of Decision. Subsection (g) calls for a “proposed plan, for review by the Secretaries, to appropriately suspend, revise, or rescind any regulations or procedures that unduly burden such projects and are not necessary to protect the public interest or otherwise comply with the law.” This ROD implements initial actions in response to Executive Order 14181. Click here for the Reclamation Long Term Operations page,  here for response to the Trump Action 5 gambit from California Department of Water Resources, and here for the response from the State Water Resources Control Board

Record-High Specific Conductance and Water Temperature in San Francisco Bay during Water Year 2015

U.S. Geological Survey (USGS) | February 22nd, 2017

The San Francisco estuary is commonly defined to include San Francisco Bay (bay) and the adjacent Sacramento–San Joaquin River Delta (delta). The U.S. Geological Survey

The San Francisco estuary is commonly defined to include San Francisco Bay (bay) and the adjacent Sacramento–San Joaquin River Delta (delta). The U.S. Geological Survey (USGS) has operated a high-frequency (15-minute sampling interval) water-quality monitoring network in San Francisco Bay since the late 1980s (Buchanan and others, 2014). This network includes 19 stations at which sustained measurements have been made in the bay; currently, 8 stations are in operation (fig. 1). All eight stations are equipped with specific conductance (which can be related to salinity) and water-temperature sensors. Water quality in the bay constantly changes as ocean tides force seawater in and out of the bay, and river inflows—the most significant coming from the delta—vary on time scales ranging from those associated with storms to multiyear droughts. This monitoring network was designed to observe and characterize some of these changes in the bay across space and over time. The data demonstrate a high degree of variability in both specific conductance and temperature at time scales from tidal to annual and also reveal longer-term changes that are likely to influence overall environmental health in the bay. In water year (WY) 2015 (October 1, 2014, through September 30, 2015), as in the preceding water year (Downing-Kunz and others, 2015), the high-frequency measurements revealed record-high values of specific conductance and water temperature at several stations during a period of reduced freshwater inflow from the delta and other tributaries because of persistent, severe drought conditions in California. This report briefly summarizes observations for WY 2015 and compares them to previous years that had different levels of freshwater inflow.

Recovery Plan for Sacramento-San Joaquin Delta native fishes

U.S. Fish and Wildlife Service (FWS) | November 26th, 1996

Eight fish species are included in the Sacramento-San Joaquin Delta Native Fishes Recovery Plan. The delta smelt is listed as a threatened species. The Sacramento splitta

Eight fish species are included in the Sacramento-San Joaquin Delta Native Fishes Recovery Plan. The delta smelt is listed as a threatened species. The Sacramento splittail (splittail) was proposed as a threatened species on January 6, 1994. This recovery plan will recommend restoration criteria for the splittail that would be appropriate recovery criteria should the species be listed. Longfin smelt, green sturgeon, spring-run, late fall-run, and San Joaquin fall-run chinook salmon are species of concern for which restoration criteria are recommended. Information is also included on Sacramento perch, a species believed to be extirpated from the Delta at this time. Habitat Requirements and Limiting Factors: The eight species included in this recovery plan depend on the Sacramento-San Joaquin Delta for a significant segment of their life history. Threats to the Delta ecosystem and these species include loss of habitat due to increased freshwater exports resulting in increased salinity, loss of shallow-water habitat due to dredging, diking and filling, introduced aquatic species that have disrupted the food chain, and entrainment (movement offish by currents produced by diversions) in State, Federal and private water diversion. State and Federal water projects have also changed the pattern and timing of flows through the Delta. The salmon races are affected by sport and commercial harvest as well as by interactions with hatchery stocks. Recovery and Restoration Objective: Delisting of delta smelt. Restoration of splittail, longfin smelt, green sturgeon, spring-run, late fall-run, San Joaquin fall-run chinook salmon, and Sacramento perch. Recovery and Restoration Criteria: Recovery criteria are quantifiable and species specific and can be used to (1) monitor effectiveness of recovery actions, (2) determine when a species has recovered to a secure level (stabilized), and (3) determine when a species qualifies for delisting. In many cases, criteria are based on two independent measures: population abundance and geographic distribution. For each species a historic base period was established using available data to characterize abundance and distribution during a pre-decline period. The time period over which abundance and distribution criteria must be met was set at five generations. For five of the eight species there is an additional requirement of meeting the criteria through a minimum number of years of stressful environmental conditions. Action Needed: 1. Enhance and restore aquatic and wetland habitat in the Sacramento-San Joaquin River estuary. 2. Reduce effects of commercial and recreational harvest. 3. Reduce effects of introduced aquatic species on Delta native fishes. 4. Change and improve enforcement ofregulatory mechanisms. 5. Conduct monitoring and research on fish biology and management requirements. 6. Assess recovery management actions and re-assess prioritization of actions. 7. Increase public awareness of importance of Delta native fishes.

Reducing Methylmercury Accumulation in the Food Webs of San Francisco Bay and Its Local Watersheds

San Francisco Estuary Institute (SFEI) | April 8th, 2014

San Francisco Bay (California, USA) and its local watersheds present an interesting case study in estuarine mercury (Hg) contamination. This review focuses on the most pr

San Francisco Bay (California, USA) and its local watersheds present an interesting case study in estuarine mercury (Hg) contamination. This review focuses on the most promising avenues for attempting to reduce methylmercury (MeHg) contamination in Bay Area aquatic food webs and identifying the scientific information that is most urgently needed to support these efforts.

Regional Monitoring Program (RMP) Field Sampling Report 2016

San Francisco Estuary Institute (SFEI) | June 1st, 2017

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is the primary source for long-term contaminant monitoring information for the Bay. The RMP

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is the primary source for long-term contaminant monitoring information for the Bay. The RMP is an innovative and collaborative effort among the scientific community, the San Francisco Bay Regional Water Quality Control Board (Water Board), and the regulated discharger community. The Program was initiated by the Water Board as a pilot study in 1989 and has been collecting water, sediment, and bivalve tissue data since its official inception in 1993. Regular monitoring of sport fish tissue and bird eggs for toxic contaminants was incorporated into the Program in 1997 and 2006, respectively.

Regional Monitoring Program (RMP) for Water Quality in San Francisco Bay, 2020 Detailed Workplan and Budget

San Francisco Estuary Institute (SFEI) | December 1st, 2019

Regional Monitoring Program (RMP) for Water Quality in the San Francisco Bay, Multi-Year Plan 2020 Annual Update

San Francisco Estuary Institute (SFEI) | January 6th, 2020

In 1992 the San Francisco Bay Regional Water Board passed Resolution No. 92-043 directing the Executive Officer to send a letter to regulated dischargers requiring the

In 1992 the San Francisco Bay Regional Water Board passed Resolution No. 92-043 directing the Executive Officer to send a letter to regulated dischargers requiring them to implement a regional multi-media pollutant monitoring program for water quality (RMP) in San Francisco Bay. The Water Board’s regulatory authority to require such a program comes from California Water Code Sections 13267, 13383, 13268 and 13385. The Water Board offered to suspend some effluent and local receiving water monitoring requirements for individual discharges to provide cost savings to implement baseline portions of the RMP, although they recognized additional resources would be necessary. The Resolution also included a provision that the requirement for a RMP be included in discharger permits. The RMP began in 1993, and over ensuing years has been a successful and effective partnership of regulatory agencies and the regulated community.