Concentrations, Loads, and Associated Trends of Nutrients Entering the Sacramento–San Joaquin Delta, California

University of California, Davis (UC Davis) | December 15th, 2021

Statistical modeling of water-quality data collected at the Sacramento River at Freeport and San Joaquin River near Vernalis, California, USA, was used to examine trends

Statistical modeling of water-quality data collected at the Sacramento River at Freeport and San Joaquin River near Vernalis, California, USA, was used to examine trends in concentrations and loads of various forms of dissolved and particulate nitrogen and phosphorus that entered the Sacramento–San Joaquin River Delta (Delta) from upstream sources between 1970 and 2019. Ammonium concentrations and loads decreased at the Sacramento River site from the mid-1970s through 1990 because of the consolidation of wastewater treatment and continuously reduced from the mid-1970s to 2019 at the San Joaquin River site. Current ammonium concentrations are mostly below 4 µM (0.056 mg N L–1) at both sites, a concentration above which reductions in phytoplankton productivity or changes in algal species composition may occur. The Sacramento River at Freeport site is located upstream of the Sacramento Regional County Sanitation District’s treatment facility’s discharge point; nutrient water quality there is representative of upstream sources. Inorganic nitrogen (nitrate plus ammonium) concentrations and loading differed at both sites. At the Sacramento River location, concentrations decrease in the summer agricultural season, reducing the molar ratios of nitrogen to phosphorus. In contrast, inorganic nitrogen concentrations increase in the San Joaquin River during the agricultural season as a result of irrigation runoff, increasing the molar ratio of nitrogen to phosphorus. This increase suggests a possible nitrogen limitation in the northern Delta and a phosphorus limitation in the southern Delta, as indicated by the molar ratios of bioavailable nitrogen to bioavailable phosphorus. Planned upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) will reduce inorganic nitrogen inputs to the northern Delta. Consequently, the supply of bioavailable nitrogen throughout the upper estuary should diminish. Source modeling of nitrogen and phosphorus identifies agriculture, atmospheric deposition, and wastewater effluent as sources of total nitrogen in the Central Valley. In contrast, geologic sources, agriculture, and wastewater discharge are the primary sources of phosphorus.

Conceptual model for salinity in the Central Valley and Sacramento-San Joaquin Delta

Central Valley Drinking Water Policy Workgroup | July 13th, 2007

This report examines the state of knowledge about the causes of salinity increase in the system and opportunities to improve the Delta as a source of municipal and agricu

This report examines the state of knowledge about the causes of salinity increase in the system and opportunities to improve the Delta as a source of municipal and agricultural water supply. It begins with background information about salinity, its measurement, and its impacts. Following that, we present observed salinity in the Bay-Delta system. The conceptual models section, the core of this report, then seeks to explain the forces and processes (drivers) that cause the salinity patterns we observe. The computational models section introduces some of the tools available to assist with salinity management and planning. The last chapter explores the implications of the conceptual model for monitoring and management of salinity.

Conceptual Model to Support PCB Management and Monitoring in the Emeryville Crescent Priority Margin Unit

San Francisco Estuary Institute (SFEI) | April 3rd, 2017

The 2014 update of the RMP PCB Strategy called for a multi-year effort to implement the recommendations of the PCB Synthesis Report (Davis et al. 2014) pertaining to: 

The 2014 update of the RMP PCB Strategy called for a multi-year effort to implement the recommendations of the PCB Synthesis Report (Davis et al. 2014) pertaining to:  1. identifying margin units that are high priorities for management and monitoring,  2. development of conceptual models and mass budgets for margin units downstream of watersheds where management actions will occur, and  3. monitoring in these units as a performance measure.  The goal of the effort is to inform the review and possible revision of the PCB TMDL and the reissuance of the Municipal Regional Permit for Stormwater (MRP), both of which are tentatively scheduled to occur in 2020. Conceptual model development for four priority margin units (PMUs) that are high priorities for management and monitoring will provide a foundation for establishing effective and efficient monitoring plans to track responses to load reductions and will also help guide planning of management actions. The Emeryville Crescent (the Crescent) is the subject of this report and the first PMU to be studied. 

Conceptual Model to Support PCB Management and Monitoring in the San Leandro Bay Priority Margin Unit Final Report

San Francisco Estuary Institute (SFEI) | November 2nd, 2019

The goal of this report is to answer three questions related to management and monitoring of PCBs in priority margin units. To this end, a conceptual model was develope

The goal of this report is to answer three questions related to management and monitoring of PCBs in priority margin units. To this end, a conceptual model was developed that includes four major elements: 1. loading from the watersheds; 2. initial deposition and retention; 3. processes determining the long-term fate of PCBs in sediment and water; and 4. bioaccumulation in the food web

Conceptual Model to Support PCB Management and Monitoring in the San Leandro Bay Priority Margin Unit, Phase One

San Francisco Estuary Institute (SFEI) | June 1st, 2018

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.

Confirmation of Initial Incidental Take for Adult Delta Smelt for the 2018 Water Year

U.S. Fish and Wildlife Service (FWS) | January 4th, 2018

Contaminant Concentrations in Eggs of Double-crested Cormorants and Forster's Terns from San Francisco Bay: 2002-2012

San Francisco Estuary Institute (SFEI) | May 2nd, 2016

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) conducted an Exposure and Effects Pilot Study (EEPS) to monitor contaminant exposure and ef

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) conducted an Exposure and Effects Pilot Study (EEPS) to monitor contaminant exposure and effects in Bay wildlife. Avian egg monitoring is one tool that was piloted in the EEPS and retained as an element of RMP Status and Trends monitoring. Avian eggs from two species have been monitored: Double-crested Cormorants (Phalacrocorax auritus), a sentinel species for the open waters of the Bay, and Forster’s Terns (Sterna forsteri), a sentinel species for shallow-water habitats on the Bay margins, including managed ponds.

Contaminant Concentrations in Sport Fish from San Francisco Bay, 2014

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

This summary report presents results from a 2014 survey of contaminants in San Francisco Bay sport fish, as well as an additional 2015 sampling of sport fish in Artesian

This summary report presents results from a 2014 survey of contaminants in San Francisco Bay sport fish, as well as an additional 2015 sampling of sport fish in Artesian Slough in Lower South Bay. This monitoring effort represents the seventh round of sport fish contaminant monitoring conducted by the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP). This technical report is intended for agency staff charged with managing water quality issues related to bioaccumulation of contaminants in San Francisco Bay.  The RMP began sport fish monitoring in 1997, following a pilot study conducted by the Bay Protection and Toxic Cleanup Program in 1994. Data collected through this monitoring program provides updates on the status and long-term trends of contaminants in Bay sport fish, and are used to update human health consumption advisories and evaluate the effectiveness of regulatory and management efforts to reduce the impacts of contaminants of concern in the Bay. Key analyses in this report include comparisons of concentrations to human health and regulatory thresholds, spatial trend evaluation, and temporal trend evaluation.  Mercury, polychlorinated biphenyls (PCBs), dioxins, selenium, polybrominated diphenyl ethers (PBDEs), and perfluoroalkylated substances (PFASs) were analyzed across sixteen fish species collected at eight locations in San Francisco Bay and Artesian Slough. Fish species were selected based on a number of criteria, including species that are popular for consumption, are sensitive indicators of problems (accumulating relatively high concentrations of contaminants), are widely distributed, represent different exposure pathways (benthic vs. pelagic), and have been monitored in the past. Concentrations were compared to numeric human health thresholds established by the California Office of Environmental Health Hazard Assessment (OEHHA) for mercury, PCBs, selenium, and PBDEs. Results were also compared to regulatory thresholds for mercury, PCBs, and selenium, as well as non-regulatory screening value for dioxins, which have been established in Total Maximum Daily Load (TMDL) regulations by the San Francisco Bay Regional Water Quality Control Board (Water Board). 

Contaminant Effects on California Bay-Delta Species & Human Health

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

Many contaminants in the California Bay-Delta exceed regulatory standards, impact aquatic species, and potentially affect human health. Recent studies provide evidence th

Many contaminants in the California Bay-Delta exceed regulatory standards, impact aquatic species, and potentially affect human health. Recent studies provide evidence that contaminants impact species of concern in the Bay-Delta (e.g., the decline of several important fish species referred to as the “Pelagic Organism Decline”). Multiple chemicals impair processes at cellular and physiological levels (measured as growth, development, and behavior abnormalities), ultimately affecting populations. As an important example, the population decline of the endangered delta smelt (Hypomesus transpacificus) is significantly associated with multiple stressors, including insecticide use. New analyses presented in this paper show significant correlations between pyrethroid (an insecticide) use and declining abundance of POD fish species. Water sampled from the Bay-Delta causes multiple harmful effects in fish and delta smelt. Fish prey items are also impacted by contaminants; this may have an indirect effect on their populations. Co-occurrence with thermal changes or disease can worsen contaminant effects. Contaminants also pose threats to human health via consumption of fish, drinking water, and contact recreation, in particular, mercury, toxins, disinfection byproducts, pesticides, pharmaceuticals, and personal care products. The role of contaminants in the decline of Bay-Delta species is difficult to accurately assess in a complex, dynamic system. However, tools and approaches are available to evaluate contaminant impacts on Bay-Delta species, and separate the effects of multiple stressors. Integrated monitoring and focused mechanistic studies are instrumental for addressing management needs. Impact and risk assessments should be conducted for different species across multiple life stages, with emphasis on early life stages of high-priority Bay-Delta species.  

Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations 2018 Update

San Francisco Estuary Institute (SFEI) | September 3rd, 2018

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) has been investigating contaminants of emerging concern (CECs) since 2001. CECs can be broad

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) has been investigating contaminants of emerging concern (CECs) since 2001. CECs can be broadly defined as synthetic or naturally occurring chemicals that are not regulated or commonly monitored in the environment, and have the potential to enter the environment and cause adverse ecological or human health impacts.