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 and Numerical Models of Dissolved Solids in the Colorado River, Hoover Dam to Imperial Dam, and Parker Dam to Imperial Dam, Arizona, California, and Nevada

U.S. Geological Survey (USGS) | August 28th, 2018

Conceptual and numerical models were developed to understand and simulate monthly flow-weighted dissolved-solids concentrations in the Colorado River at Imperial

Conceptual and numerical models were developed to understand and simulate monthly flow-weighted dissolved-solids concentrations in the Colorado River at Imperial Dam. The ability to simulate dissolved-solids concentrations at this location will help the Bureau of Reclamation satisfy the binational agreement on the volume and salinity of Colorado River water delivered to Mexico. A robust spatial- and temporal-resolution dataset that consists of river discharge and dissolved-solids concentration and load information between January 1990 and September 2016 for 10 sites on canals, drains, tributaries, and the main stem of the Colorado River between Hoover and Imperial Dams was generated. Daily mean dissolved-solids concentrations were estimated and monthly mean dissolved-solids loads were computed for each site. Spatial and temporal load patterns, and historical and current controls on loads and concentrations, were analyzed in order to develop a conceptual model of dissolved- solids transport between Hoover and Imperial Dams. Two numerical models describing the relations between dissolved- solids concentrations and components controlling dissolved-solidsconcentrations and loads were developed, calibrated, and verified. Between January 1990 and September 2016, there was a 98.8-million-acre-feet loss of water and a 57.0-million-ton loss of dissolved-solids load from the Colorado River between Hoover and Imperial Dams. Between Hoover and Parker Dams, about 69.0 million acre-feet of water was lost and 51.1 million tons of dissolved solids were lost; between Parker and Imperial Dams, about 29.8 million acre-feet of water was lost and 5.9 million tons of dissolved solids were lost. Water was removed from the river at a relatively consistent rate over the 25-year study period through water transfers to California and Arizona, evapotranspiration from crop irrigation, transpiration processes of riparian vegetation, and evaporation from the river main stem. Dissolved solids were removed from the river between Hoover and Parker Dams at a relatively constant rate through water transfers to California and Arizona, and water pumped from the river for irrigation within the Mohave Valley. A small amount of dissolved solids are gainedby the river from inflow from the Bill Williams River. Between Parker and Imperial Dams, however, dissolved solids were not removed from the river at a consistent rate over the study period. Dissolved solids were generally removed from the river from 1990 to 2012, then gained by the river from 2012 to 2015, and then removed from the river from 2015 through 2016. Dissolved solids are assumed to be removed from the river and accumulated within the floodplain sediments and aquifers during irrigation processes; some dissolved solids may also be removed from the river through uptake by crops and riparian vegetation. Dissolved solids accumulated on the landscape and in the floodplain aquifer during irrigation are transported to the river during periods when the hydraulic gradient between the floodplain aquifer and the river is increased, causing a gain in dissolved solids in the river. Dissolved-solids gains in the river occur during periods of relatively low river discharge, such as during the winter months and during drier climatic conditions. Two numerical models were developed and coefficientswere estimated by using data from a May 2008-September 2016 calibration period. One model simulates concentrations at Imperial Dam based on the Colorado River system downstream from Parker Dam, and the other model simulates concentrations at Imperial Dam based on the Colorado River system downstreamfrom Hoover Dam. Both models simulated monthly flow-weighted concentrations of dissolved solids for the Colorado River at Imperial Dam, which corresponded well with observed concentrations for the entire study period. The models are more sensitive to input variables of monthly discharge of the ColoradoRiver below Parker Dam and monthly flow-weighted dissolved-solids concentrations of the Colorado River below Hoover Dam and Parker Dam than to the rate of change in concentration with respect to time and the combined discharge of the Colorado River Indian Reservation Main Canal and the Palo Verde Canal. The calibrated models can be used to run scenarios of future monthlyflow-weighted dissolved-solids concentrations in the ColoradoRiver at Imperial Dam. Although the models are expected to provide concentration estimates within 18 milligrams per liter (Parker Dam to Imperial Dam model) to 22 milligrams per liter (Hoover Dam to Imperial Dam model), 95 percent of the time, the error of future scenarios increases as uncertainty in the estimated future input variables increases.

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.

Condition of California Perennial, Wadeable Streams Based on Algal Indicators

Southern California Coastal Water Research Project | October 1st, 2013

Algae can serve as indicators of stream ecological condition in two ways. Information about algal community composition can be used for bioassessment analogous to the

Algae can serve as indicators of stream ecological condition in two ways. Information about algal community composition can be used for bioassessment analogous to the way in which benthic macroinvertebrates (BMIs) are employed (e.g., as described in Ode et al. 2011). When algae occur in excess (i.e., in the case of eutrophication), stress to the system can result; as such, the total amount of algae present also becomes an indicator of stream health in its own right. To date, the state of California has invested in several initiatives to build capacity for conducting stream algal assessment. This includes support for creation of a planning document funded by State Water Resources Control Board’s (SWRCB) Surface Water Ambient Monitoring Program (SWAMP) (Fetscher and McLaughlin 2008) and establishment of SWAMP Standard Operating Procedures (SOPs) for field sample collection (Fetscher et al. 2009) and a laboratory processing and enumeration SOP (currently in review) for determining algal community composition. In addition, an algae Index of Biotic Integrity (IBI) for bioassessment of southern California streams was recently completedby Fetscher et al. (2013), and a state algae laboratory, based at California State University San Marcos, has been established. Over the past several years, the state of California’s Perennial Stream Assessment (PSA)and Reference Condition Management Program (RCMP), the southern California Stormwater Monitoring Coalition (SMC), and other smaller programs have collected and processed algae samples using the SWAMP protocols. As such, a substantial amount of standardized data on stream algae and instream, vascular macrophytes (together hereafter referred to as stream “primary producer indicators”) have been collected in California since 2007. However, no consolidated analysis of these data has been conducted so far. This report represents such an effort.

Confined Animal Facility Permitting and Reporting Under the Porter-Cologne Water Quality Control Act: An Analysis of Regional Board Activities

Stanford University | February 2nd, 2026

This white paper analyzes reports containing (1) data from 2023 for the five regions with the largest numbers of CAFs in California; and (2) data from 2024 from the regio

This white paper analyzes reports containing (1) data from 2023 for the five regions with the largest numbers of CAFs in California; and (2) data from 2024 from the region with the most CAFs in the state. We identify six central problems with the self-reporting regime: CAFs frequently underreport wastewater production, or fail to report it at all. CAFs frequently underreport manure production. CAFs do not disclose, or inadequately document, where waste goes. Most CAFs fail to report how much waste they apply to their crops. (Those that do typically report significant overapplication.) CAFs frequently fail to account for all nutrients in the waste they produce. Regional Boards do not adequately enforce reporting requirements.

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

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

Considerations for Management of the Mouth State of California’s Bar-built Estuaries

Southern California Wetlands Recovery Project | January 10th, 2019

Bar-built estuaries are the dominant estuary type in California, and many of these small estuaries are subject to closure with a sand barrier separating a lagoon

Bar-built estuaries are the dominant estuary type in California, and many of these small estuaries are subject to closure with a sand barrier separating a lagoon estuary from the ocean for days, months or even years. In the lagoon impounded behind the sand barrier, water levels may rise or fall depending on net water budget and water quality extremes may develop. These conditions and the obstruction of fish passage motivate managed breaching of the sand barrier in many systems statewide – an intervention that alleviates or preempts environmental problems, but which also can result in undesirable secondary impacts due to the acute effect of a single breach or the chronic effect of repeated breaching over years. Management decisions are based on an implicit trade-off between anticipated benefits and costs that depend on the values and priorities of stakeholders. This report was written to provide an overview of considerations for managed breaching in California. It presents a synthesis of processes and phenomena related to mouth closure and breaching in general and uses this to identify potential impacts of breaching, without intending any judgment of which impacts are more or less desirable. Three specific systems are reviewed in detail: Los Peñasquitos Lagoon in San Diego County, Scott Creek Estuary in San Mateo County and Russian River Estuary in Sonoma County. While there are fundamental similarities in the closure and breaching cycle across all bar-built estuaries statewide, there is also an immense diversity between these systems due to differences in size, in hydrology (wet north to dry south), and in development (rural, urban, agricultural, road/rail). The local community is likely to develop the best management strategy where there is significant effort and experience in local monitoring, science, and stakeholder consultation. However, where there is limited monitoring, science or consultation, the considerations outlined in this report provide preliminary guidance – and comparison with one of the study systems can provide more specific insight to the potential impacts of breaching management decisions. We synthesize current understanding related to how mouth state influences estuary functions and conditions, which in turn affect ecological services. While both natural and managed breaching affect many processes and phenomena in the estuary, breaching events and managed breaching regimes do not occur in isolation and many other factors affect the estuary functions and conditions, including freshwater inputs, the adjacent landscape, and stressors in the watershed. However, managed breaching is one of very few short-term management options and therefore a valuable adaptive management tool, specifically in systems that are already perturbed or impacted by human encroachment. Although emergency breaches may be required in rare occasions, our recommendation is to develop a breaching strategy for specific systems in which breaching has been used or in which it is likely to be used as a management tool. In this context, we recommend ways in which science can provide improved support for management decisions and identify a few systems in California in which there is already a well-developed, science-based management plan. Associated document: "Wetlands on the Edge: The Future of Southern California's Wetlands - Regional Strategy 2018"