Water and Suspended-Sediment Flux Measurements at the Golden Gate, 2016-2017

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

Sediment is an important resource for San Francisco Bay (SFB), in the context of restoration projects, dredging operations, ecosystem health, and contaminant transport an

Sediment is an important resource for San Francisco Bay (SFB), in the context of restoration projects, dredging operations, ecosystem health, and contaminant transport and fate. Understanding the transport and fate of sediment in SFB is important to ecosystem researchers and managers. Previous studies have shown that sediment exchange at the estuary-ocean boundary of SFB (Golden Gate inlet) is the most poorly understood element of the SFB sediment budget, owing to logistical challenges that inhibit routine field observations, and the fact that net flux is a small fraction of the instantaneous peak values experienced on a daily basis. Improved understanding of sediment exchange at the estuary-ocean boundary of SFB is essential to updating SFB-wide sediment budgets, which account for sources, sinks, and storage of sediment (and sediment-associated contaminants). In this study, field observations of water and suspended-sediment fluxes at the Golden Gate were made over one ebb tide and one flood tide on three occasions: 1) 21-22 March 2016, following a large storm event that triggered the first flow into Yolo Bypass flood control structure since 2011 2) 23 June of 2016, during a period of low freshwater inflow; 3) 27-28 February 2017, following several large storms of the wettest winter in northern California in recorded history.

Water and the COVID-19 Pandemic Impacts on Municipal Water Demand

Pacific Institute | July 2nd, 2020

Water and the Future of the San Joaquin Valley

Public Policy Institute of California (PPIC) | February 14th, 2019

The San Joaquin Valley—California’s largest agricultural region and an important contributor to the nation’s food supply—is in a time of great change. The valle

The San Joaquin Valley—California’s largest agricultural region and an important contributor to the nation’s food supply—is in a time of great change. The valley is ground zero for many of California’s most difficult water management problems—including groundwater overdraft, drinking water contamination, and declines in habitat and native species. Local water supplies are limited, particularly in the southern half of the region. To irrigate their crops, many farmers use water imported from the Sacramento–San Joaquin Delta. But in many places farmers have also relied on groundwater overdraft—pumping groundwater in excess of the rate at which it is replenished. Worsening droughts, increasing regulations to protect endangered native fishes, and growing demand by Southern California for Delta imports have compounded surface water scarcity. The state’s Sustainable Groundwater Management Act (SGMA) requires local water users to bring groundwater use to sustainable levels by the early 2040s. This will have a broad impact on valley agriculture and the regional economy in coming years—likely including some permanent idling of farmland. This report explores three key challenges facing the San Joaquin Valley and reviews the most promising approaches to address them:  Balancing water supplies and demands. To close the groundwater deficit, groundwater sustainability agencies in the valley’s overdrafted basins will have to augment supplies, reduce demands, or use some combination of these two approaches. A range of options are under consideration but they are not equally effective or practical.  Addressing groundwater quality challenges. Poor groundwater quality impairs drinking water supplies in disadvantaged rural communities, reduces long-term agricultural prosperity, and degrades ecosystems. Providing safe drinking water is an urgent priority. Over the longer term, parties will also need to manage water quantity and quality together, to take advantage of synergies and avoid unintended consequences. The necessary coordination will be challenging because the various programs addressing valley water quality issues are carried out by numerous local and regional entities, whose lines of responsibility and geographic boundaries do not neatly align.  Fostering beneficial water and land use transitions. Effectively addressing water scarcity and the resulting land use changes in the San Joaquin Valley offers opportunities to put lands coming out of production to good use—and gain “more pop per drop” from limited water resources. Multiple-benefit approaches to water and land management can enhance groundwater recharge and improve air and water quality. They can also promote healthier soils, new recreational opportunities, additional flood protection, improved habitat, and new revenue streams for private landowners engaging in conservation-oriented management. Addressing these complex and intertwined issues requires significant changes in water and land management and a major ramp-up in cooperation and coordination among a wide circle of stakeholders. Pursuing solutions that deliver multiple benefits will boost the chances of success overall. The entire region—and California as a whole—will benefit if solutions to these challenges are cost-effective and support the valley’s economy while improving public health and the natural environment.

Water Column Selenium Concentrations in the San Francisco Bay-Delta: Recent Data and Recommendations for Future Monitoring

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

The San Francisco Bay Regional Water Board developed a Total Maximum Daily Load (TMDL) and implementation plan for selenium in North San Francisco Bay (NSFB) in 2015.1 T

The San Francisco Bay Regional Water Board developed a Total Maximum Daily Load (TMDL) and implementation plan for selenium in North San Francisco Bay (NSFB) in 2015.1 The TMDL is based on attainment of water column and fish tissue target concentrations protective of human health, aquatic life, and wildlife, and was approved by the US Environmental Protection Agency in August, 2016. Analyses in support of the TMDL synthesized the results of different monitoring efforts to characterize selenium concentrations in water and biota in the Estuary. For water quality evaluation in the TMDL, the sources of observational data included studies of selenium speciation across the estuarine salinity gradient, performed in 1999-2000 and again in 2010 and 2012 (Cutter and Cutter 2004, Doblin et al. 2006, Tetra Tech, 2012), as well as samples collected by the San Francisco Bay Regional Monitoring Program (RMP). Changes in wastewater treatment from the five major refineries in NSFB were implemented in the late 1990s, leading to significant reductions in selenium loads. Data at Estuary center-line locations showed small changes for dissolved selenium in the mid-salinity range and no trends in particulate selenium (Baginska, 2015). As part of the TMDL, water quality modeling analyses were performed to characterize NSFB selenium concentrations under a range of hydrologic conditions and changing point-source loads (Baginska, 2015). Water column selenium concentration data in the NSFB and Delta continue to be collected at selected locations, although these data have not been systematically evaluated following the analyses presented in the TMDL reports. In the near term, possible changes that may cause selenium concentrations to change in the NSFB and Delta include concentration changes in the inflow from the San Joaquin River basin, changes in refinery inputs, changes in stormwater and tributary loads from the Bay margin, and changes in overall Central Valley hydrological conditions, such as the extreme wet and dry periods that occurred between 2012 and 2017. Other drivers, such as nutrient concentrations and algal levels, may also play a role, especially on the concentrations of selenium on particulates.

Water Quality Assessment of the Condition of California Coastal Waters and Wadeable Streams: Clean Water Act Section 305b Report 2006

California State Water Resources Control Board (SWRCB) | July 25th, 2006

One of the first steps in managing our environmental resources is to determine their current condition by answering the key question, “What is the overall condition of

One of the first steps in managing our environmental resources is to determine their current condition by answering the key question, “What is the overall condition of California’s surface waters?” Often-raised questions relating to the condition of our waters include, “Is the water safe to drink?” “Are the waters safe to swim?” “Are the fish safe to eat?” “Is aquatic life healthy?” The condition assessments presented in this report focus on two waterbody types: coastal bays and estuaries and wadeable perennial streams. The assessments in this report focus on the question “Is aquatic life healthy?” The “aquatic life” use designation in California’s water quality control plans refers to the beneficial uses of waters that support either warm-water or cold-water ecosystems, including fish, wildlife, invertebrates, vegetation, and other components of aquatic ecosystems. While historical assessments of water quality have primarily focused on describing chemical water quality, this report includes assessments based on biological indicators when available. This report includes assessments of the condition of coastal bays and estuaries and wadeable perennial streams statewide based on data collected through the Environmental Monitoring and Assessment Program led by the U.S. Environmental Protection Agency (U.S. EPA). These statewide assessments represent the state’s initial attempt to make broad statistical estimates of the conditions of these waterbody types. It establishes baselines against which to compare future assessments. All the statewide assessments based on Environmental Monitoring and Assessment Program datasets have known levels of certainty. These confidence intervals are not included in this report but are available in the technical reports cited. The statewide assessments rely on data from a survey design that generates statistically defensible, unbiased assessments of the conditions of these waterbody types. As such, they did not specifically focus on areas of high impact. Other sampling, which has targeted such areas have shown toxicity and elevated chemical levels in some areas. In addition, only a limited set of indicators were used for the assessments. These indicators are specified in each section. The federal Clean Water Act’s Section 305b requires each state to report on the quality condition of its waters. The California State Water Board submits its water quality condition assessment report biennially to the U.S. Environmental Protection Agency (U.S. EPA). The reports submitted by states serve as the basis for U.S. EPA’s National Water Quality Inventory Report to Congress. The Inventory Report is the primary report for the public about the condition of the nation’s waters. The report is also used to inform water quality management decisions, including the allocation of certain Clean Water Act funds among states. However, key reviews of national and state monitoring and assessment efforts suggest that the National Water Quality Inventory Report does not accurately portray water quality conditions, that the monitoring done by states does not always allow for valid assessments of water quality condition in unmonitored waters, and that a consistent approach to monitoring and data collection is needed to support core water programs (U.S. Government Accounting Office, 2000; National Research Council, 2001).  As a result, the information provided on the status and trends of waters at statewide and at national scales may be inadequate to support decision making. The water quality condition assessment reports submitted thus far by California have been based on a regional approach to reporting. The approach corresponds to the structure of the nine California Regional Water Boards and provides essential information for specific waterbodies. However, the assessments cannot be successfully integrated into an accurate statewide report because regions use a variety of assessment approaches and do not always apply criteria consistently. Also, due to limited resources, monitoring has generally focused on problem identification. Clean waters were less likely to be targeted for monitoring, and assessments were based on data with a bias towards sites that were likely sampled due to suspected problems. Furthermore, assessments could not be extrapolated to unmonitored waterbodies or those with insufficient data. That there is no current way to develop a valid national picture of water quality condition speaks both to the monitoring and assessment challenges faced by states as well as the need for improved assessment tools. The California Water Boards have actively taken steps to meet these challenges. The Surface Water Ambient Monitoring Program’s (SWAMP) comprehensive monitoring and assessment strategy describes some of these steps (A comprehensive monitoring and assessment strategy to protect and restore California’s water quality.  Surface Water Ambient Monitoring Program. 2005. [http://www.waterboards.ca.gov/swamp/reports.html]). As part of the strategy, SWAMP has partnered with U.S. EPA on large-scale monitoring efforts through the Environmental Monitoring and Assessment Program. The Environmental Monitoring and Assessment Program October 2006 Clean Water Act Section 305b Report 2006: California Water Quality Condition Assessment Report effort relies on a statistical monitoring approach that allows assessments of the condition of waters to be extrapolated to unmonitored areas. For 2006, U.S. EPA has agreed that California can use a different format to submit and meet its Clean Water Act Section 305b reporting requirements. This report would include assessments based on an evaluation of California data collected under U.S. EPA’s Environmental Monitoring and Assessment Program. The assessments apply to two waterbody types: (1) coastal bays and estuaries and (2) wadeable perennial streams. “Wadeable” streams are streams, creeks, and small rivers that are shallow enough to sample without boats. The assessments focus on one beneficial use (aquatic life use) and are based on a limited suite of key indicators. Specifically, the report had to include sections summarizing: • Statewide assessments of coastal bays and estuaries based on California data collected as part of the Environmental Monitoring and Assessment Program for Coastal Waters. • Statewide assessments of wadeable perennial streams based on aquatic invertebrate data collected in California as part of the Environmental Monitoring and Assessment Program for Inland Surface Waters. • Assessments of northern and southern coastal California’s wadeable perennial streams based on aquatic invertebrate data collected in these areas as part of the Environmental Monitoring and Assessment Program for Inland Surface Waters. When available, assessments from large-scale regional monitoring efforts such as the Regional Monitoring Program for San Francisco Bay, the Central Coast Long-Term Environmental Assessment Network, the Southern California Bight Project, and the Surface Water Ambient Monitoring Program have been included. Specifically, more detailed assessments of the San Francisco Bay, the Central Coast, and the Southern California Bight areas are included as part of the coastal waters assessment. More detailed assessments of the Santa Clara River Watershed in Southern California and waters in the Central Coast region are included as part of the wadeable perennial streams assessment. Brief summaries of the Regional Water Boards’ surface water ambient monitoring programs are included in the final section of this report.

Water Quality Assessment of the State Water Project, 1998-99

California Department of Water Resources (DWR) | August 10th, 2000

This report describes water quality in the State Water Project during 1998 and 1999. The Executive Summary covers important drinking water parameters such as salinity and

This report describes water quality in the State Water Project during 1998 and 1999. The Executive Summary covers important drinking water parameters such as salinity and trihalomethane precursors. The rest of the report assesses all parameters including metals and pesticides.

Water Quality Challenges in the San Francisco Bay/ Sacramento-San Joaquin Delta Estuary: EPA’s Action Plan

U.S. Environmental Protection Agency (EPA) | August 22nd, 2012

The U.S. Environmental Protection Agency (EPA) developed this Action Plan after assessing the effectiveness of current regulatory mechanisms designed to protect water qua

The U.S. Environmental Protection Agency (EPA) developed this Action Plan after assessing the effectiveness of current regulatory mechanisms designed to protect water quality in the San Francisco Bay Sacramento-San Joaquin Delta Estuary (Bay Delta Estuary) and its tributaries. EPA’s assessment concludes that Clean Water Act (CWA) programs currently are not adequately protecting aquatic resources of the Bay Delta Estuary. In this document, EPA recommends actions to restore water quality for aquatic species protection using existing EPA authorities and resources, as well as actions EPA believes are important and appropriate for the State Water Resources Control Board (State Water Board). EPA is one of more than 25 state and federal governmental agencies with responsibilities in the Bay Delta Estuary. EPA’s major statutory mission in the Estuary is to implement the CWA. EPA has delegated many CWA program authorities to the State Water Board while providing financial support,1 technical assistance, and oversight (including, in some cases, review and approval of State actions). Much of EPA's work in this Action Plan (as well as elsewhere in California) is done in support of and in partnership with the State. For example, water quality standards, which define water quality goals for our waterbodies, are typically developed and adopted by the State with EPA assistance, review, and ultimately, approval or disapproval. In the Bay Delta Estuary, EPA focuses on assuring that the many designated uses of the Estuary’s aquatic resources are protected. EPA emphasizes the CWA goals of maintaining and improving water quality – the chemical, physical, and biological integrity of the water – to ensure the Bay Delta Estuary can function as a vibrant, healthy estuary. About 90 species of fish are found in the Delta. The Delta’s channels serve as a migratory route and nursery area for Chinook salmon, striped bass, white and green sturgeon, American shad, and steelhead trout. These anadromous fish spend most of their adult lives either in the lower bays of the Estuary or in the ocean. Resident fish in the Estuary include delta smelt, longfin smelt, Sacramento splittail, catfish, largemouth bass, black bass, crappie, and bluegill. All Bay Delta Estuary waters are impaired by one or more contaminants. In addition, the reduction in the quantity and quality of estuarine habitat limits the Estuary’s ability to support aquatic species. EPA’s Action Plan describes a suite of activities to: 1. Strengthen water quality standards to protect estuarine habitat 2. Advance regional water quality monitoring and assessment 3. Accelerate water quality restoration through Total Maximum Daily Loads 4. Strengthen selenium water quality criteria 5. Prevent pesticide pollution 6. Restore aquatic habitats while managing methylmercury 7. Support the Bay Delta Conservation Plan Collectively, these activities will contribute to the restoration of the Bay Delta Estuary. Even if they are all successfully implemented, however, they are not sufficient to resolve the complex problems that have stressed the ecosystem to the point of collapse. Any solution to the ecological problems of the Bay Delta Estuary must be multi-faceted, including providing sufficient flows, physical habitat which is sufficiently large, connected, diverse, and self-sustaining, as well as a reduction of many types of stressors, such as contaminants, invasive species, and predation.

Water Quality Conditions in the Sacramento-San Joaquin Delta and Suisun and San Pablo Bays during 2009

California Department of Water Resources (DWR) | December 28th, 2010

This report summarizes the results of water quality monitoring and special  studies conducted by the Environmental Monitoring Program (EMP) within the Sacramento-San Joa

This report summarizes the results of water quality monitoring and special  studies conducted by the Environmental Monitoring Program (EMP) within the Sacramento-San Joaquin Delta (Delta) and Suisun and San Pablo bays (the upper San Francisco estuary) during calendar year 2009. This monitoring is mandated by Water Right Decision 1641 (D-1641) and this report is being submitted to fulfill the reporting requirements of this decision. The EMP monitored water quality using a protocol implemented in 1996. Under this monitoring protocol, 13 sampling sites—2 of which were added after 1996—representing 8 regions of the upper San Francisco estuary (estuary) were monitored for 15 physical and chemical water quality parameters. The results gathered from the sampling of these 15 parameters are described in this report. Parameters such as water temperature, Secchi disk depth, dissolved oxygen (DO) concentration, specific conductance, dissolved inorganic nitrogen, orthophosphate, and volatile suspended solids were within their historical range. Measured parameters exhibited seasonal variation as well as changes in response to significant rainfall events and in flow rates. In addition to monitoring physical and chemical water quality parameters, biological sampling was conducted to monitor the productivity and community composition of phytoplankton, zooplankton, and benthic communities.

Water Quality Conditions in the Sacramento-San Joaquin Delta during 1995

California Department of Water Resources (DWR) | August 1st, 1999

Water year 1995 was a wet year, ending an eight-year period of predominantly dry and critically dry years.  After a relatively dry fall, January and March precipitation

Water year 1995 was a wet year, ending an eight-year period of predominantly dry and critically dry years.  After a relatively dry fall, January and March precipitation was heavy and produced flooding in the Central Valley.  By May 1, precipitation was 165% of average, snowpack water content was 215% af average, seasonal runoff was 170% of average, and reservoir storage was 110% of average. In 1995, the Net Delta Outflow Index (NDOI) was used to estimate Delta outflow, and the Sacramento and San Joaquin River Unimpaired Runoff indices were used to determine water year type for 1995.  Using these indices, water year 1995 was officially classified as wet on May 1, 1995.  All standards, including those in Water Right Decision 1485, as amended by the 1995 Water Quality Control Plan, were met in 1995. The entire 1995 calendar year was characterized by excess conditions, and both State Water Project and Central Valley Project water requirements were met as well as in-Delta consumptive uses.  Delta outflows were high throughout the year, and the calculated average monthly flows exceeded 80,000 cubic feet per second (CFS) during the peak outflow period (January through May), and 3,000 cfs during the minimum outflow period (July through November).

Water Quality Control Plan for Salinity (draft)

California State Water Resources Control Board (SWRCB) | October 15th, 1988