San Francisco Bay Nutrients Project

San Francisco Bay Water Board staff has embarked on an effort working with staff at the San Francisco Estuary Institute (SFEI) to develop nutrient numeric endpoints (NNE) for the San Francisco Bay Estuary. This effort is part of a statewide initiative, supported by the U.S. EPA Region IX and the State Water Board, to address nutrient over-enrichment (eutrophication) in State waters, specifically to develop the NNE framework for streams and lakes and for California’s coastal estuaries.  The process for developing nitrogen and phosphorus nutrient criteria for California started in 1998 with the publication of the U.S. Environmental Protection Agency’s National Strategy for the Development of Regional Nutrient Criteria (USEPA, 1998). A key goal of this project is to develop a set of NNEs that can be used by the Water Board in our water quality programs. To receive email updates about this project, visit our email subscription page and sign up for the "Nutrients in San Francisco Bay" email list.

The Concern about Nutrients in San Francisco Bay

Excess nutrients in lakes, rivers, or estuaries can cause a range of environmental impacts associated with the unwanted growth of algae and other microscopic organisms generally classified as phytoplankton. Nitrogen is the primary nutrient of interest for estuaries like San Francisco Bay, which stimulates phytoplankton production under the right conditions. This stimulus can increase the risk of harmful algae blooms and associated toxins. Conversely, phytoplankton decomposition consumes oxygen necessary for fish survival and a healthy ecosystem and can result in fish kills.

San Francisco Bay receives some of the highest nitrogen loads among estuaries worldwide yet does not experience the severe impacts common to other nutrient-enriched estuaries. Researchers contribute this phenomenon to high suspended sediment concentrations, phytoplankton consumption by clams, and rapid mixing of the Bay's windswept waters. However, recent observations have identified substantial shifts in the Bay's response, or sensitivity, to nutrients based on long-term monitoring data. The Nutrient Management Strategy (NMS) has revealed other water quality conditions, including recurring low dissolved oxygen (DO) in some margin habitats and consistent detection of toxins produced by harmful algae. Their effects on human and ecological health require evaluating and determining the linkage to human-derived nutrients.

Factors influencing the Bay's response to nutrients include suspended sediment concentrations, light availability, freshwater inputs, and ocean conditions. These factors are 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 long-term increases in nutrient loading and plausible scenarios leading to eutrophication-driven degradation.

The San Francisco Bay Nutrient Management Strategy and its Key Participants

The SF Bay Regional Water Quality Control Board formed the Nutrient Management Strategy (NMS) in 2014, following an effort of the State Water Resources Control Board to develop Numeric Nutrient Endpoints instead of Water Quality Objectives for nitrogen and phosphorus. The Regional Water Board convened the NMS in recognition that consequential nutrient-related management decisions will benefit from a multistakeholder process. In response, the Regional Water Board prioritized the development of a locally supported, multi-interest, long‐term science strategy and associated implementation program to inform nutrient‐related management decisions affecting SF Bay.

A Steering Committee comprised of a diverse range of decision-makers guides the implementation of the NMS Science Program, information sharing, and public outreach related to nutrient management in SF Bay. The NMS's outputs and outcomes inform the ongoing development of policy regulating nutrient discharges from wastewater facilities and other sources. All of the work reports produced through the NMS associated with the themes described below are available on a tracking website. The SF Bay Nutrient Watershed Permit for Municipal and Industrial Wastewater Dischargers (NPDES No. CA0038873) formally articulates these policies.

Key Science Questions

Fundamentally, the NMS Science Program must characterize current and future risks of eutrophication-driven degradation associated with human contributions of nutrients. To that end, the San Francisco Estuary Institute and collaborators currently focus on several main themes:

Nutrient loading to the Bay, transport, and transformation

Few other estuaries worldwide receive higher nutrient loads, measured on an areal basis, compared to San Francisco Bay. The region's forty-two water resource recovery facilities 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 during the previous several years, corresponding with population trends.

Nutrient losses from the SF Bay water column occur through transformations mediated by phytoplankton, other microbes, and transport. 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.

Low DO conditions in the margins and sloughs

The conceptual model for phytoplankton dynamics in SF Bay points to light 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 and 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 algal species

Since 2015, the NMS has 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. Scientists place nutrient levels among the main factors that favor HAB events, though establishing the mechanistic link between HABs and nutrients has proven challenging in estuaries worldwide. Domoic acid concentrations in SF Bay mussels have generally been much lower than human consumption advisory levels. In contrast, concentrations of microcystin and saxitoxin have approached and sometimes exceeded consumption advisory levels.

The NMS funded a pilot study in 2018 focusing on the northern anchovy - the most abundant fish in SF Bay and an important food resource for fish, bird, and mammal species to characterize toxin levels further. All three toxins were detected in composite anchovy samples, with detection frequencies of 96%, 25%, and 13% for DA, MCY, and STX, respectively. The NMS is evaluating molecular approaches to more efficiently track HABs.

Breaking - HAB Event of Summer 2023

During the summers of 2022 and 2023, San Francisco Bay has experienced a large bloom of the species, Heterosigma akashiwo, one of several species that can cause water to take on a reddish-brown color, commonly called “red tide”. The Water Board is working through the Nutrient Management Strategy team to track observations of algae or wildlife impacts to understand the scope of the bloom. For more information, see these answers to frequently asked questions about this HAB event.

Because of our regulatory program and Nutrient Management Strategy, scientists are able to mobilize quickly to study this bloom and emergency funding has already been allocated to support monitoring this bloom. Over the past several years, major investments augmenting our capacity to monitor algal blooms include the following:

  • Systematic collection of algal toxin data during recurring channel cruises
  • Development of DNA-sequencing techniques for specific algal species
  • Sampling for algal species of concern and their toxins during lateral mapping surveys
  • Measurement of algal toxins in bivalves at several location

Coastal impacts

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.
Tools for planning next steps

Assessment framework – Development of a process to understand impairment

Assessment frameworks are a type of management tool used to evaluate and communicate information relating to the state of an ecosystem. They are used commonly around the world and in multiple disciplines to assess the status of a system using key indicators that provide robust estimates of ecological conditions. In addition, these frameworks can connect to management actions implemented based on a system's status. An assessment framework to characterize nutrient status in San Francisco Bay is under development, with input from expert advisors and stakeholders. This effort follows a California State Water Resources Control Board (State Water Board) funded initiative to develop expert-informed assessment criteria for nutrients in deep subtidal habitats of San Francisco Bay, known as Nutrient Numeric Endpoints, or NNEs.

A step towards developing an assessment framework for nutrients in SF Bay is establishing a suite of numeric endpoints that indicate the Bay's response to nutrient over-enrichment or eutrophication, such as algal biomass or DO. The endpoints guide the translation of narrative water quality objectives for nutrients and biostimulatory substances. A final assessment framework is slated for completion in 2023 to inform the third iteration of the Nutrient Watershed Permit.

Long term monitoring and modeling – Development of a sustainable program to track trends

One central NMS focus area involves developing numerical models to simulate the physics and biogeochemistry of SF Bay and applying those models to answer applied science and management questions related to nutrient transport, cycling, and the ecosystem responses to nutrients. Recent applications of the model include determining the relative contributions of nutrients from individual point sources within subregions of the Bay, considering both nutrient transport and transformations within the system. The NMS-derived model builds on lessons from complementary modeling efforts and leverages funding to model the northern Estuary and outer coast. Additional model applications include testing outcomes associated with load management scenarios, similar to the recent SFEI-led study to test the Delta's response to the Sac Regional upgrade; changes in operations of managed salt ponds; or testing water quality response to future scenarios.

In addition to developing a world-class coupled hydrodynamic and water quality model, the NMS seeks to leverage lessons learned in the Chesapeake Bay region and elsewhere to implement next-generation tools to track water quality trends. Through collaboration with the Chesapeake Bay Program, Tampa Bay Estuary Program and US Berkeley, the NMS developed a novel application of generalized additive models (GAMs) for characterizing multi-decadal changes in water quality indicators on a long-term or seasonal basis and to better characterize the uncertainly associated with those trends. A web-based dashboard was developed to communicate these trends, with a hope to utilize this tool for routine reporting and communications to a broader range of stakeholders.

Future scenarios – How evolving 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.

For more information contact:
Richard Looker
San Francisco Bay Regional Water Quality Control Board
1515 Clay Street, Suite 1400
Oakland, CA 94612
Phone: 510-622-2451