An Introduction to High-Frequency Nutrient and Biogeochemical Monitoring for the Sacramento– San Joaquin Delta, Northern California

U.S. Geological Survey (USGS) | July 11th, 2017

This report is the first in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Jo

This report is the first in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Joaquin Delta of northern California (Delta). This first report provides an introduction to the reasons for and fundamental concepts behind collecting HF measurements, and describes the benefits associated with a real-time, continuous, HF, multi-parameter water quality monitoring station network that is co-located with flow stations. It then provides examples of how HF nutrient measurements have improved our understating of nutrient sources and cycling in aquatic systems worldwide, followed by specific examples from the Delta. These examples describe the ways in which HF instrumentation may be used for both fixed-station and spatial assessments. The overall intent of this document is to describe how HF measurements currently (2017) are being used in the Delta to examine the relationship between nutrient concentrations, nutrient cycling, and aquatic habitat conditions.

Assessment of Nutrient Status and Trends in the Delta in 2001–2016: Effects of drought on ambient concentrations and trends

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

Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP)

Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP). The Program’s first assessment question regarding nutrients is: “How do concentrations of nutrients (and nutrient-associated parameters) vary spatially and temporally?” In this analysis, we confirmed previously reported declining trends in the San Joaquin River for nutrient concentrations at Vernalis and chlorophyll-a concentrations at Buckley Cove and Disappointment Slough. A slight increasing trend for dissolved oxygen at Buckley Cove was also detected which could be confirmation that management actions for the San Joaquin River Dissolved Control Program are having the desired effect. Finally, at stations in Suisun Bay, the Confluence region, and Franks Tract, chlorophyll-a showed modest increasing trends, which were not evident in previous analyses. The new analyses presented in this report and the findings from earlier reports constitute encouraging early progress toward answering the Delta RMP’s assessment questions. Specifically, due to the existence of long-term data sets and synthesis efforts, spatial and temporal trends in the concentrations of nutrients and nutrient-related parameters are reasonably well understood and so are the magnitudes of the most important sources of nutrients from outside the Delta. However, additional synthesis work could be done to understand the factors behind these trends. Large knowledge gaps remain about nutrient sinks, sources, and processes within the Delta. The mechanistic, water quality-hydrodynamic models being developed for the Delta may be able to address these questions in the future.

Biology-based Stressor Thresholds

California State Water Resources Control Board (SWRCB) | October 1st, 2011

The objective of this memo is to describe how biological assessment data (such as those collected using Surface Water Ambient Monitoring Program (SWAMP) bioasse

The objective of this memo is to describe how biological assessment data (such as those collected using Surface Water Ambient Monitoring Program (SWAMP) bioassessment protocols) can be used to develop biologically-relevant stressor thresholds. This memo describes an objective approach for setting regulatory stressor thresholds based on the association between biological condition and stressor intensity gradients. While these relationships show a large amount of variability typical of biological data, there are clear thresholds that indicate levels below or above which stream health is maintained or degraded.

Blurred lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California

Harmful Algae (Elsevier) | March 10th, 2018

San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are

San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are few commercial fishery harvests within SFB, recreational and subsistence harvesting for shellfish is common. Coastal shellfish are monitored for domoic acid and paralytic shellfish toxins (PSTs), but within SFB there is no routine monitoring for either toxin. Dinophysis shellfish toxins (DSTs) and freshwater microcystins are also present within SFB, but not routinely monitored. Acute exposure to any of these toxin groups has severe consequences for marine organisms and humans, but chronic exposure to sub-lethal doses, or synergistic effects from multiple toxins, are poorly understood and rarely addressed. This study documents the occurrence of domoic acid and microcystins in SFB from 2011 to 2016, and identifies domoic acid, microcystins, DSTs, and PSTs in marine mussels within SFB in 2012, 2014, and 2015. At least one toxin was detected in 99% of mussel samples, and all four toxin suites were identified in 37% of mussels. The presence of these toxins in marine mussels indicates that wildlife and humans who consume them are exposed to toxins at both sub-lethal and acute levels. As such, there are potential deleterious impacts for marine organisms and humans and these effects are unlikely to be documented. These results demonstrate the need for regular monitoring of marine and freshwater toxins in SFB, and suggest that co-occurrence of multiple toxins is a potential threat in other ecosystems where freshwater and seawater mix.

Characterizing and quantifying nutrient sources, sinks and transformations in the Delta: synthesis, modeling, and recommendations for monitoring

San Francisco Estuary Institute (SFEI) | January 5th, 2016

The Sacramento-San Joaquin Delta (the Delta) receives high loads of the nutrients nitrogen (N) and phosphorous (P) from wastewater treatment effluent and agricultural run

The Sacramento-San Joaquin Delta (the Delta) receives high loads of the nutrients nitrogen (N) and phosphorous (P) from wastewater treatment effluent and agricultural runoff. Flows from the Sacramento River, San Joaquin River, and other tributaries transport these loads through a complex network of rivers, channels and flooded islands, before entering San Francisco Bay. Excessive loads of N and P can adversely impact ecosystem health by causing excessive algal blooms and low dissolved (Valiela et al, 1992; Kamer and Stein 2003). Excessive nutrients may also contribute to the occurrence of harmful algal blooms (Bates et al, 1989) and overgrowth of nuisance aquatic macrophytes (Valiela et al, 1992). Major nutrient management decisions are being considered in both the Delta and San Francisco Bay, and those decisions require the best-available science to understand the factors that regulate ambient conditions, and the effects of loads and ambient conditions on ecosystem health. A mechanistic and quantitative understanding of nutrient cycling and fate in the Delta is essential both for informed decisions related to current conditions and also because of major anticipated changes in both loads to the Delta (upgrades at wastewater treatment facilities) and habitat function due to restoration efforts and water management. We hypothesized that the Delta is an important biogeochemical reactor, and that transformations or losses strongly regulate ambient nutrient concentrations within the Delta and modulate nutrient loads to San Francisco Bay. Both N and P have complex cycles and require careful investigation. In this paper, we focus on nitrogen, including loads, cycling, and losses or transformations that influence its ultimate fate.

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.

Delta Regional Monitoring Program Nutrients Synthesis: Modeling to Assist Identification of Temporal and Spatial Data Gaps for Nutrient Monitoring

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

Nutrient loads are an important water quality management issue in the Sacramento-San Joaquin Delta (Delta) and there is consensus that the current monitoring activities d

Nutrient loads are an important water quality management issue in the Sacramento-San Joaquin Delta (Delta) and there is consensus that the current monitoring activities do not collect all the information needed to answer important management questions.  The purpose of this report is to use hydrodynamic model outputs to refine recommendations for monitoring nutrients and related conditions in the Delta. The basic premise was that variability in water source and hydraulic residence time can serve to estimate variability in water quality. Therefore, using existing hydrodynamic models that are highly resolved in space and time could be a cost-effective way to get information about likely spatial and temporal variability in nutrients and nutrient-associated parameters. We assume that the Delta can be divided into relatively homogeneous subregions (e.g., such as those proposed in a previous report by Jabusch et al. 2016) and that a representative monitoring location can be chosen in each subregion to track status and trends. We also assume that, within any subregion, areas with long hydraulic residence time and source water mixing may represent potential nutrient transformation hotspots.  Two types of modeling approaches were applied: 1) volumetric water source analysis to evaluate the mix of source waters within each subregion; and 2) particle tracking simulations. Results from the source water analysis were evaluated to assess heterogeneity of water sources within each of the subregions. Results from the particle tracking analysis were evaluated to identify high-residence-time areas. Finally, we compared analysis results to current monitoring locations to inform potential monitoring gaps or redundancies within each of the subregions. 

Designing a High-Frequency Nutrient and Biogeochemical Monitoring Network for the Sacramento–San Joaquin Delta, Northern California

U.S. Geological Survey (USGS) | July 11th, 2017

This report is the third in a series of three reports that provide information about how high-frequency (HF) nutrient monitoring may be used to assess nutrient inputs and

This report is the third in a series of three reports that provide information about how high-frequency (HF) nutrient monitoring may be used to assess nutrient inputs and dynamics in the Sacramento–San Joaquin Delta, California (Delta). The purpose of this report is to provide the background, principles, and considerations for designing an HF nutrient-monitoring network for the Delta to address high-priority, nutrient-management questions. The report starts with discussion of the high-priority management questions to be addressed, continues through discussion of the questions and considerations that place demands and constraints on network design, discusses the principles applicable to network design, and concludes with the presentation of three example nutrient-monitoring network designs for the Delta. For three example network designs, we assess how they would address high-priority questions that have been identified by the Delta Regional Monitoring Program (Delta Regional Monitoring Program Technical Advisory Committee, 2015). This report, along with the other two reports of this series (Kraus and others, 2017; Downing and others, 2017), was drafted in cooperation with the Delta Regional Monitoring Program to help scientists, managers, and planners understand how HF data improve our understanding of nutrient sources and sinks, drivers, and effects in the Delta. The first report in the series (Kraus and others, 2017) provides an introduction to the reasons for and fundamental concepts behind using HF monitoring measurements, including a brief summary of nutrient status and trends in the Delta and an extensive literature review showing how and where other research and monitoring programs have used HF monitoring to improve our understanding of nutrient cycling. The report covers the various technologies available for HF nutrient monitoring and presents the different ways HF monitoring instrumentation may be used for both fixed station and spatial assessments. Finally, it presents numerous examples of how HF measurements are currently (2017) being used in the Delta to examine how nutrients and nutrient cycling are related to aquatic habitat conditions.

Dissolved Oxygen in South San Francisco Bay: Variability, Important Processes, and Implications for Understanding Fish Habitat

San Francisco Estuary Institute (SFEI) | October 30th, 2018

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Inst

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Institute (SFEI) launched a study to investigate the potential effects of low-DO on habitat quality in Lower South Bay (LSB) to inform decisions about nutrient regulation. The goal of the study was to understand where and when regions of LSB provide adequate DO to support resident fish species. The study approach involved convening a team of experts to advise on methods, analyzing high frequency DO measurements from seven mooring stations in LSB, and partnering with researchers from UC Davis to interpret several years of monthly fish abundance data in LSB relative to DO and other factors.

Estuary News, December 2008

San Francisco Estuary Partnership (SFEP) | December 15th, 2008