Nutrients in San Francisco Bay
Our Team in the Nutrients in San Francisco Bay
The San Francisco Estuary Institute comprises over sixty scientists, technologists, and designers who offer a wide range of expertise. Each team member, in her or his own way, helps to define environmental problems, advance public debate about them through sound science, and support consensus-based solutions that improve environmental planning, management, and policy development.
Projects Related to the Nutrients in San Francisco Bay
SF Bay Nutrients Visualization Tool
This visualization tool facilitates intuitive comparison of continuous data from around the Bay, and across a variety of analytes, to demonstrate the potential for collaborative monitoring across programs.
Publications related to the Nutrients in San Francisco Bay
The Institute has collectively produced more than 1300 reports, articles, and other publications over the course of its 24-year existence. The following list represents those publications associated with this individual program and its focus areas.
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Year of Publication: 2015
. Dissolved Oxygen in Sloughs of San Francisco Bay. Richmond, CA; 2015. 
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(2.86 MB) Year of Publication: 2014
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San Francisco Bay Nutrient Management Strategy
San Francisco Bay, among the world's most nutrient-rich estuaries, faces elevated risk from high levels of nitrogen and phosphorus. This abundance of nutrients can negatively affect water quality and habitat health, fueling excessive growth of algae or phytoplankton in a process known as eutrophication. The repercussions can be severe, leading to depleted oxygen levels, which stress aquatic life, and the emergence of toxic algae.
Credit: Adobe Stock.The Bay Area is served by over 40 wastewater facilities, catering to the needs of over 7.5 million residents. These facilities treat and discharge over 500 million gallons of effluent to the Bay daily, contributing the majority of nutrient loads. Despite their effectiveness at removing many pollutants, most facilities were not originally designed to extract nutrients. As such, these facilities contribute about 50,000 kg of nitrogen to the Bay each day.
San Francisco Bay showed impressive resistance to its high nutrient loads for many years. Until the summer of 2022, the Bay managed to avoid severe or persistent impacts that typically afflict other nutrient-rich estuaries. This perception changed following the unprecedented bloom of Heterosigma akashiwo, a harmful algae species, spreading from the Central Bay to most other Bay sub-embayments from July to September, 2022. This marked a significant shift in the Bay's nutrient response dynamics, adding a new layer of complexity to our understanding of its ecosystem.
While factors such as high levels of suspended sediment, strong tides, and dense populations of filter-feeding clams in certain regions have historically buffered the Bay against the effects of eutrophication, the recent H. akashiwo bloom suggests a possible change. Research and monitoring over the past 10-20 years have indicated shifts in the Bay's sensitivity to nutrients, and the 2022 bloom, which unfolded again in the summer of 2023, heightens concerns that the Bay’s resilience to elevated nutrients may be waning.
In response to scientific concerns of a growing threat, the San Francisco Bay Nutrient Management Strategy (NMS) was launched in 2014. The San Francisco Estuary Institute (SFEI) spearheads the scientific efforts under this strategy, collaborating with a network of scientists. The mission is clear - to determine the potential adverse impacts of human-sourced nutrients on the Bay's ecosystem and establish what management actions or load reductions are necessary to prevent or mitigate potential harm, both now and in the future.
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Building a framework for an integrated HAB detection and monitoring system in San Francisco Estuary | Over the last decade, harmful algal blooms (HABs) have emerged as one of the highest-priority water quality management issues in the San Francisco Estuary, which includes the... |
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Nature Based Solutions for Nutrient Removal | High nutrient concentrations can cause increased phytoplankton biomass, low dissolved oxygen, and increased harmful algal blooms and toxins, with detrimental effects on... |
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SF Bay Nutrients Visualization Tool | This visualization tool facilitates intuitive comparison of continuous data from around the Bay, and across a variety of analytes, to demonstrate the potential for... |
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Water Quality Monitoring & Synthesis
San Francisco Bay benefits from one of the longest-running water quality monitoring programs of any estuary worldwide. Since 1969 the U.S. Geological Survey (USGS) has monitored water quality along a 145-kilometer-deep water transect that spans from the Golden Gate to the Delta.
This data has revealed substantial changes in the Bay’s response to high nutrient levels in recent decades. In addition, special studies, expanded monitoring, and modeling conducted since the formation of the Nutrient Management Strategy (NMS) revealed other water quality conditions (e.g., recurring low dissolved oxygen in some margin habitats and consistent detection of multiple toxins produced by harmful algae) whose effects on human and ecological health require evaluation and determination of causal factors. Efforts are also underway to monitor harmful algae using genetic tools.
In 2013, the NMS initiated a Moored Sensor Program to collect nutrient-related water quality data at high temporal frequency to complement ship-based monitoring of water quality indicators, quantify tidal, daily, and longer-term biogeochemical dynamics, and allow for improved calibration of biogeochemical models. In the last decade, the NMS has expanded to 11 stations, distributed across various habitats in South Bay and Lower South Bay, with new stations planned for the Central Bay.
Factors influencing the Bay’s response to nutrients include suspended sediment concentrations, light availability, freshwater inputs, and ocean conditions. These factors are themselves variable due to local land and water management and climate oscillations. The number of variables involved demands a wide range of monitoring, modeling, and research efforts to understand ongoing and potential trajectories of change in water quality and ecosystem response resulting from increasing nutrient loading rates and plausible scenarios leading to eutrophication-driven degradation.
Modeling Nutrient Effects
One of the central themes of the Nutrient Management Strategy (NMS) is the development of advanced numerical models to simulate the complex interactions of physics and biogeochemistry in San Francisco Bay. These models are crucial for addressing practical science and management questions related to nutrient dynamics and their impact on the ecosystem.
Recent applications of these models have allowed us to pinpoint the specific contributions of nutrients from individual point sources within different subregions of the Bay. This comprehensive approach takes into account both the transport of nutrients and their transformations within the Bay's intricate system. The NMS-derived model builds upon the knowledge gained from other modeling initiatives and benefits from collaborative efforts, including modeling efforts focused on the Delta and outer coast.
Furthermore, our models are versatile and can be used for various purposes. For instance, we have used them to evaluate different scenarios, such as the impact of load management strategies. A recent study, led by SFEI, tested how changes in the operation of managed salt ponds and potential future scenarios could affect water quality.
In addition to model development, the NMS is committed to adopting innovative approaches to track water quality trends. Drawing inspiration from successful initiatives in regions like the Chesapeake Bay and Tampa Bay, we have harnessed the power of generalized additive models to analyze multi-decadal changes in water quality indicators, considering both long-term and seasonal variations. To enhance accessibility and communication, we've created a web-based dashboard that displays these trends. We aim to use this tool for regular reporting and to engage a wider range of stakeholders in our efforts.
Assessing Nutrient Effects for San Francisco Bay
Assessment frameworks are valuable management tools used to quantify and convey information about the condition of an ecosystem. They are widely employed across various disciplines and regions to evaluate the health of a system by analyzing key indicators that offer robust insights into ecological conditions. Moreover, these frameworks serve as a bridge to connect management actions with the current state of the ecosystem.
Currently, there is an ongoing effort to develop an assessment framework specifically tailored to assess the nutrient status of San Francisco Bay. This effort is split into two complementary parts, focusing on deep subtidal portions of San Francisco Bay and the shallow Lower South Bay. This initiative involves the active participation of expert advisors and stakeholders. It is an extension of a project funded by the California State Water Resources Control Board, which aimed to establish expert-informed assessment criteria for nutrients in the deep subtidal habitats of San Francisco Bay, known as Nutrient Numeric Endpoints (NNEs).
A critical step in crafting this nutrient assessment framework for SF Bay is establishing a set of numeric endpoints. These endpoints indicate how the Bay responds to nutrient over-enrichment or eutrophication, such as changes in algal biomass, toxin concentrations, or dissolved oxygen levels. These numeric endpoints are pivotal in translating narrative water quality objectives for nutrients and biostimulatory substances into tangible, measurable terms. Ultimately, the finalized assessment framework will provide valuable insights for regulatory and management decisions regarding nutrient discharges from wastewater treatment plants or other sources and help ensure the Bay's environmental well-being.
Nutrient loading, transport, and transformation
Few other estuaries worldwide receive higher nutrient loads, measured on an area basis, compared to San Francisco Bay. The region's forty-two Publicly Owned Treatment Works (POTWs) account for >60% of dissolved inorganic nitrogen and dissolved inorganic phosphate inputs to the system, with higher levels in portions of the Bay. Nutrient loading from municipal sources has increased over the last two decades, with levels plateauing over the previous several years, corresponding with population trends.
Nutrient losses from the SF Bay water column occur through transformations mediated by phytoplankton and other microbes and transport. These processes affect the specific forms of nitrogen and phosphorus within the water column yet do not remove nutrients entirely from the system. The primary pathways for loss of nutrients from the system include denitrification in anoxic sediment and transport to other regions of SF Bay or the coastal ocean. The NMS supports the ongoing development of a world-class hydrodynamic and water quality model to inform the Bay's response to nutrient loading and the consequences of scenarios, including nutrient loading rates, changes in sediment concentrations, and climate-induced temperature shifts.
Phytoplankton Production and Oxygen Status
The conceptual model for phytoplankton dynamics in SF Bay points to light, not nutrients, as the dominant factor controlling phytoplankton production, given the high nutrient concentrations present year-round and variable sediment concentrations that limit light penetration into the water column. In the deep channel, phytoplankton biomass generally remains low year-round, except during relatively short-lived stratification events that allow suspension of phytoplankton near the surface.
Conditions along the shallow shoals foster higher growth rates and high biomass without stratification because the shallow water column creates greater average light levels. Periods of high suspended sediment concentrations or consumption by clams or other 'grazers' represent exceptions to this rule. Several sloughs of the Lower South Bay exhibit prolonged and significant sags in dissolved oxygen concentrations though managers and the public rarely observe fish kills. Recent studies point to unnaturally high oxygen consumption rates in some Lower South Bay slough habitats, particularly those connected to salt ponds (e.g., Alviso Slough and Guadalupe Slough).
Harmful Algae and Toxin Production
Starting in 2015, the Nutrient Management Strategy (NMS) began monitored concentrations of harmful algal toxins in mussels collected from the perimeter of the Bay every two weeks. The NMS and other researchers have documented frequent detections of harmful algal bloom (HAB) forming organisms and their associated toxins, including saxitoxin, domoic acid, and microcystin. Domoic acid concentrations in SF Bay mussels are generally much lower than human consumption advisory levels. In contrast, concentrations of microcystin and saxitoxin have approached and sometimes exceeded consumption advisory levels.
For decades, researchers noted the resiliency of SFB to high nutrient loads and large-scale HAB events. Before the summer of 2022, SFB had not experienced severe HAB events or other persistent impacts common to other nutrient-enriched estuaries. This changed following the extraordinary Heterosigma akashiwo bloom that spread from the Central SF Bay to most other portions of SF Bay in July to September 2022.
SFB’s historic resistance to high-nutrients stems from multiple factors, including high suspended sediment concentrations which decreases light delivery to phytoplankton; strong tides that thoroughly mix the water column, which further limits light availability, and replenishes oxygen levels in deeper waters); and dense populations of filter-feeding clams in some regions of SF Bay that maintain phytoplankton at relatively low levels.
Preliminary work indicates physical factors triggered the formation of the 2022 H. akashiwo bloom, which managed to consume all nutrients in a significant portion of Central and South SF Bay. The bloom triggered unprecedented oxygen demand, where dissolved oxygen levels fell below 5 mg/l for a week and below 2 mg/l for a few days. Untold numbers of fish died likely from toxicity and lethal oxygen levels, including relatively high numbers of white and green sturgeon.
Nutrient Export and Effects on the Outer Coast
SF Bay benefits from several factors that cap phytoplankton productivity and reduce nitrogen utilization in the system, including high turbidity and strong tidal mixing. While those factors increase SF Bay's internal capacity for high nutrient concentrations, this translates into more significant nutrient exports to the coastal ocean. Model simulations suggest that, while substantial fractions of SF Bay's nitrogen loads are 'lost' via denitrification, SF Bay serves as a significant source of nitrogen to the coastal ocean via the Golden Gate. Despite the magnitude of these nitrogen loads, we currently know little about the potential effects on ecological conditions along the coast.
In collaboration with the NMS, researchers from around the state are pursuing questions regarding the transport of human-derived nutrients to the outer coast and rising concerns of HABs, ocean acidification, and decreasing oxygen levels. Coastal upwelling complicates these studies and the projections for future impacts since scientists expect climate change to increase upwelling and nutrient levels along the coast and portions of SF Bay. Resource demands of the NMS have placed most of the research and monitoring focus on the Bay rather than the outer coast. Collaborations with researchers from UCLA, UC Santa Cruz, and elsewhere enable the program to leverage world-class scientists and models to answer management questions about whether human-derived nutrients impact the ocean.
Scenario modeling to inform how management and climate change could impact the Bay
Scenarios influencing nutrient dose-response do not represent eutrophication endpoints or indicators since these can involve physical (e.g., sediment concentrations and freshwater flow), social (e.g., population growth), and climate-induced changes. However, understanding the range of circumstances under which changes to the system may result in a cascade of eutrophication-related impacts requires that the NMS characterize a variety of plausible scenarios. SF Bay has undergone rapid and unanticipated regime shifts in recent decades. To assess short- and long-term risk, the NMS must understand the critical drivers of system change (e.g., reduced turbidity, changes in ocean temperature, human population-induced nutrient load increases).
The NMS anticipates seeking agreement on the highest priority scenarios and what constitutes acceptable model skill during the current permit term, followed by refinements of scenario assessments.
High nutrient levels in San Francisco Bay make the system susceptible to water and habitat quality degradation. Observations to date include increasing levels of chlorophyll-a levels over the last two decades, low dissolved oxygen in shallow portions of Lower South Bay, and the occurrence of harmful algae and their associated toxins. Significant upgrades to the region’s wastewater infrastructure may be required if conditions worsen to reduce nutrient discharges. To help inform the potential upgrade options, the SF Bay Regional Water Quality Control Board has issued permits requiring the wastewater community to evaluate several different types of interventions.
From 2014 to 2019, the region’s wastewater agencies collaborated through the Bay Area Clean Water Agencies (BACWA) to evaluate engineered solutions for optimizing or upgrading the region’s wastewater facilities. This involved assessing opportunities to modify existing infrastructure to optimize nutrient removal or implement new technologies for advanced treatment. The current Nutrient Watershed Permit requires an evaluation of nature-based solutions for nutrient reduction, as well as the role of projected wastewater recycling efforts to divert nutrient loads away from the Bay.
The evaluation of nature-based solutions for nutrient reduction via treatment wetlands and other multi-benefit approaches is underway by SFEI through coordination between the Nutrient Science team and Resilient Landscapes Program. To date, analyses indicate some wastewater agencies may be able to leverage existing infrastructure and buffer lands to create or enhance nature-based treatment strategies that also enhance habitat value and provide flood risk reduction benefits for sea level rise adaptation purposes.