San Joaquin River Restoration Program

San Joaquin River Restoration Program | December 13th, 2007

San Joaquin River Restoration Settlement

Congressional Research Service (CRS) | November 9th, 2007

Historically, Central California’s San Joaquin River supported large Chinook salmon populations. Since the Bureau of Reclamation’s Friant Dam on the San Joaquin River

Historically, Central California’s San Joaquin River supported large Chinook salmon populations. Since the Bureau of Reclamation’s Friant Dam on the San Joaquin River became fully operational in the 1940s, much of the river’s water has been diverted for off-stream agricultural uses. As a result, approximately 60 miles of the river bed is dry in most years. Thus, the river no longer supports Chinook salmon populations in its upper reaches. In 1988, a coalition of conservation and fishing groups sued Reclamation (Natural Resources Defense Council v. Rodgers). A U.S. District Court judge has ruled that operation of Friant Dam violates state law because of its destruction of downstream fisheries. Faced with mounting legal fees, uncertainty, and the possibility of dramatic cuts to water diversions, parties negotiated a settlement instead of proceeding to trial. In September 2006, an agreement, commonly called the Settlement, was reached. It calls for new releases of water from Friant Dam to restore fisheries, as well as for efforts to mitigate reductions in off-stream deliveries lost to restoration flows. Congressional authorization and appropriations are required for full Settlement implementation. Legislation based on the Settlement (H.R. 4074, H.R. 24 and S. 27) is pending. Related bills have also been introduced. A key legislative issue is how to finance the Settlement, specifically how to resolve congressional pay-as-you-go (PAYGO) issues. Other challenges are how to achieve the Settlement’s dual goals of fisheries restoration and water management, and how to address concerns of stakeholders not party to the Settlement, without disrupting the negotiated agreement. The amount of water projected for restoration flows and the volume of reduced Friant water deliveries are related, but the relationship would not necessarily be one-for-one. Available estimates for total annual Friant water supplies (including both contract and temporary water) are, on average, 15% to 16% less under the Settlement than under current operations; but such estimates do not account for improvements in water management that might reduce the impact on water users. For three-quarters of water contractors, the reduction would represent a reduction in one of their available sources of water. The impacts of such reductions will vary by contractor depending on the firmness of existing surface water supplies and the reliability of groundwater supplies. How to offset the decrease and who would pay for investments in other water sources and improved efficiency has not been determined. Although the region may benefit from increased recreational expenditures and investment in river restoration activities under the Settlement, studies suggest its largest and mostly negative economic impact would be on the agriculture industry, at least in the short term. In addition, downsteam interests not party to the Settlement have been concerned about increased flooding, groundwater infiltration, and competition with existing federal financial commitments. Nearby communities fear harm to groundwater quantity and quality. Some of these concerns have been addressed in the legislation, but some remain. On the other hand, some communities and interests believe restoration will bring other benefits to the river, such as improved surface water quality in lower San Joaquin River reaches. Ultimate Settlement costs and benefits are very difficult to predict.

San Leandro Bay PCB Study Data Report

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

The goal of RMP PCB special studies over the next few years is to inform the review and possible revision of the PCB TMDL and the reissuance of the Municipal Regional P

The goal of RMP PCB special studies over the next few years is to inform the review and possible revision of the PCB TMDL and the reissuance of the Municipal Regional Permit for Stormwater, both of which are tentatively scheduled to occur in 2020. Conceptual model development for a set of four representative priority margin units will provide a foundation for establishing an effective and efficient monitoring plan to track responses to load reductions, and will also help guide planning of management actions. The Emeryville Crescent was the first PMU to be studied in 2015-2016. The San Leandro Bay PMU is second (2016-2017), Steinberger Slough in San Carlos is third (2017), and Richmond Harbor will be fourth (2018). The conceptual model reports for these four PMUs will be developed and presented using a consistent framework, and will build on each other to form an integrated assessment of these four areas. The lessons learned from these analyses will also be more generally applicable to similar contaminated sites on the margins of the Bay. This document is a data report on field studies to support development of a conceptual model for San Leandro Bay.

Scientific Basis Report in Support of New and Modified Requirements for Inflows from the Sacramento River and its Tributaries and Eastside Tributaries to the Delta, Delta Outflows, Cold Water Habitat, and Interior Delta Flows

California State Water Resources Control Board (SWRCB) | October 2nd, 2017

The State Water Board is conducting a review and update of the 2006 Bay-Delta Plan to ensure that beneficial uses of water in the Bay-Delta watershed are reasonably prote

The State Water Board is conducting a review and update of the 2006 Bay-Delta Plan to ensure that beneficial uses of water in the Bay-Delta watershed are reasonably protected. Phase I addresses potential changes to San Joaquin River flow requirements for the protection of fish and wildlife and potential changes to southern Delta salinity requirements for the protection of agriculture.1 Phase II addresses changes to the Bay-Delta Plan to protect native fish and wildlife in the Sacramento River, Delta, and associated tributaries. This Scientific Basis Report (Science Report or Report) is being prepared to support the Phase II update of the Bay-Delta Plan. It describes the science on which proposed changes to the Bay-Delta Plan will be based. A working draft version of the Report was released on October 19, 2016, to receive early scientific and public input on the science related to Phase II prior to submittal of the Report for external peer review. The State Water Board received input from a number of interested parties including water users; environmental groups; and local, state, and federal agencies. In recognition of the vision for “one Delta, one science” articulated in the Delta Stewardship Council’s (DSC) Delta Plan, the State Water Board also requested that the Delta Independent Science Board (Delta ISB) conduct a review of the Report. The State Water Board appreciates the valuable comments and suggestions that have helped further strengthen the scientific content in this version of the Report. In addition, comments related to regulatory and policy issues were raised that have further informed the development of proposed changes to the Bay-Delta Plan, including implementation approaches. The general components of these changes are summarized below and in more detail in Chapter 5 for context, and will continue to be refined as the planning process moves forward. This Report and the peer reviewers’ responses will be posted on the State Water Board web site and become part of the record for this Bay-Delta Plan update. Content from this Report will be included in a larger Staff Report that will also contain information on environmental, economic, and other analyses of potential changes to the Bay-Delta Plan, including regulatory and policy considerations of competing uses of water (including municipal, industrial, agricultural, power production, and other environmental uses of water such as wetland and wildlife refuge supplies). These issues are not addressed in this Science Report. Further, while a description of the approach for proposed changes to the Bay-Delta Plan is provided, the exact regulatory language is still under development and will be informed by the science in this Report and other information that will be included in the Staff Report. The public and agencies will continue to have opportunities to provide input throughout this process.

Scrutinizing the Delta Cross Channel

CALFED | June 1st, 2001

Sea level rise and the drivers of daily water levels in the Sacramento-San Joaquin Delta

Nature Portfolio (Springer Nature) | December 17th, 2023

Sediment Lithology and Borehole Erosion Testing, American and Sacramento Rivers, California

U.S. Geological Survey (USGS) | July 9th, 2020

A field investigation intended to measure the potential for erosion of sediments beside the American and Sacramento Rivers near Sacramento, California, is described. The

A field investigation intended to measure the potential for erosion of sediments beside the American and Sacramento Rivers near Sacramento, California, is described. The study featured two primary components: (1) drilling and soil sampling to reveal lithology, down to depths matching the local river thalweg, where possible, and (2) borehole erosion tests (BETs) as described by Briaud and others (2017) at many of the same locations. The latter test involved drilling a vertical hole, measuring its diameter profile, inserting a hollow drilling rod to almost the bottom of the hole, and pumping fluid through the drilling rod at a known discharge for a chosen time interval. The hole was then resurveyed to establish an erosion rate (change in borehole radius divided by duration of flow event) as a function of depth, and the test was repeated. This test was performed with water as the erosive fluid at 12 locations, with 1 test repeated with drilling mud. Lithology holes were drilled at these same locations and an additional five locations. Drilling operations took place on river left and river right on the American River and river left (left bank, when looking downstream) on the Sacramento River.

Sediment Transport in Two Tributaries to the San Joaquin River Immediately Below Friant Dam—Cottonwood Creek and Little Dry Creek, California

U.S. Geological Survey (USGS) | May 2nd, 2023

Two tributaries to the greater San Joaquin River watershed, Cottonwood and Little Dry Creeks, in California’s Central Valley, were assessed for sediment and streamflow

Two tributaries to the greater San Joaquin River watershed, Cottonwood and Little Dry Creeks, in California’s Central Valley, were assessed for sediment and streamflow dynamics between October 1, 2011, and September 30, 2019. The two systems deliver sediment to the San Joaquin River below Friant Dam, California. Dams create downstream discontinuities in streamflow and sediment transport and therefore influence fish habitat and sediment dynamics. Because these two creeks are directly downriver from Friant Dam, they become the most upstream source of sediment to the San Joaquin River below Friant Dam. The quality and quantity of spawning habitat for fish in the gravel-bedded reach of the San Joaquin River relies on a range of bed material particle size suitable for redd structure. The effects of coarse-sand to fine-gravel supply on salmonid habitat depends primarily on the size of the sediment and the timing of its addition from tributaries to the San Joaquin River; thus, understanding the timing, quantity, and size of sediment supplied from these two tributaries is critical to the management of ecological and biological sustainability. Streamflow from Cottonwood and Little Dry Creeks, along with streamflow from the San Joaquin River below Friant Dam, were compared to continuously measured water-surface elevations to quantify the timing and direction of streamflow. Suspended-sediment samples were collected with multiple automatic samplers and analyzed for concentration and grain-size distribution. Measured suspended-sediment concentrations and streamflows were used to develop sediment rating curves and compute continuous estimates of suspended-sediment load for each tributary. Satellite imagery was used to qualify spatial and temporal dynamics through the lower watersheds and support more quantitative sediment-load estimates. Computed annual sediment loads ranged from 1.32x101 to 2.68x104 metric tons for Little Dry Creek and 9.82 to 1.98x103 metric tons for Cottonwood Creek. Sediment loads computed during the study period for both watersheds show that annual loads were highest during water year 2017 (October 1, 2016, to September 30, 2017). Sediment transport primarily occurred between the months of January and March. In both tributaries, grain-size distributions of suspended sediment were predominantly coarse-sized sand and were finer than the remnant bed material. Both creeks demonstrate backwater effects from the San Joaquin River, but the more tortuous stream channel and historical mining pits within Little Dry Creek provide more capacity for sediment storage compared to the less complex stream network of Cottonwood Creek. Because loads were computed based on upstream streamgages and not at the confluence of each tributary to the San Joaquin River, annual load estimates do not represent direct flux into the San Joaquin River; instead, these results indicated that in Little Dry Creek, particularly, the lowest portion of the watershed stores sediment before it reaches the San Joaquin River.

Selenium in Muscle Plugs of White Sturgeon from North San Francisco Bay, 2015-2017

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

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) muscle tissues collected from live sturgeon

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) muscle tissues collected from live sturgeon during the California Department of Fish and Wildlife’s fall sturgeon tagging studies in North San Francisco Bay. The goal of this study was to non-lethally collect a large number of sturgeon muscle plugs and analyze them for selenium to (1) establish an understanding of current status, trends, and causes of variability in sturgeon muscle selenium concentrations; and (2) evaluate the potential for long-term sturgeon selenium monitoring with muscle plugs, through development of field and laboratory methods and informing the monitoring design. Monitoring of selenium in white sturgeon is needed to evaluate the effectiveness of the North Bay Selenium Total Maximum Daily Load (TMDL) in protecting sturgeon from selenium toxicity. This technical report provides documentation of the study and presents its major findings in the context of all historically available data on sturgeon muscle selenium concentrations in San Francisco Bay. 

Selenium in White Sturgeon from North San Francisco Bay: The 2015-2017 Sturgeon Derby Study

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

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) tissues collected during the 2015-2017 Sturg

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) tissues collected during the 2015-2017 Sturgeon Derby events in North San Francisco Bay. The goal of this study was to investigate the distribution of selenium among sturgeon tissues to inform the toxicological and regulatory interpretation of selenium measured in non-lethally collected tissues, including muscle plugs and fin rays. This technical report provides documentation of the study and presents its major findings.