The SFB Nutrient Management Strategy is being developed and implemented through a collaborative process between the Water Board and multiple partners and stakeholders. Generating the scientific understanding needed to fully support all of the management decisions and questions will likely take substantial time and significant resources, and will involve complex decisions.  This work element lays out the basic components of the program for implementing the Nutrient Strategy.

Activities Update

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Task 1.1 Develop Governance Structure

A straightforward and transparent governance and decision-making structure for Nutrient Strategy implementation is needed to

• maximize effectiveness of stakeholder input;
• identify and allocate limited resources toward research, monitoring, and modeling that will most effectively inform management decisions;
• carry out external scientific review of the overall Nutrient Strategy, the recommended approaches that are developed within key work elements (e.g., Assessment Framework, Monitoring, Modeling), and major work products
• lay out how decisions will be made, in particular on substantive issues on which reaching consensus may be difficult  

A work group will be convened to develop a work plan and scope of work for developing a governance structure for Nutrient Strategy implementation.  This may involve hiring a consultant to assist with identifying approaches that are well-suited for addressing the unique set of scientific, regulatory, and economic issues related to nutrient concerns in San Francisco Bay.

Task 1.2 Develop Funding Plan

While this document focuses in detail on activities that should be completed during the next 5 years, implementation of the Nutrient Strategy work elements will likely be a carried out over a substantially longer period.  The cumulative costs of sustaining the nutrient-related research, monitoring, and modeling are anticipated to be high. SFB is an ecosystem of regional, state-wide, and national significance, and a valued resource for both the public and private sectors. As such, a funding plan will be developed that casts a wide net, targeting resources from federal science agencies (e.g., NSF, NOAA), state funding, and foundations, as well as developing partnerships with other SFB science and monitoring programs, and partnerships with regional university and research institutes.  This task involves developing initial costs estimates of the work, developing a funding plan, and on-going fundraising.  

Task 1.3 Nutrient Program Management

This task involves managing the Nutrient Strategy implementation. Activities will include scientific oversight, stakeholder engagement, coordinating SAG meetings, coordinating external scientific review, information dissemination, fundraising, and overall program management (e.g., overseeing projects, project and contract management).  

There are no specific subtasks for Task 1.3. 

Activities Update

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Task 2.1 Develop Conceptual Models of Ecosystem Response to Nutrient Loads

The goal of this task is to develop conceptual models for SFB that characterize important processes linking nutrient and organic matter loading, biological responses, and indicators of adverse effects of nutrient over-enrichment.

The approach to nutrient objectives proposed for San Francisco Bay involves: 1)  the use of response indicators to diagnose adverse effects from nutrient overenrichment in  an assessment framework 2) the use of models to link response indicators to nutrient loads that will sustain and protect beneficial uses. The conceptual models developed in this task are needed to confirm appropriate indicators and their linkages to SF Bay beneficial uses; identify the spatial and temporal scales of importance in monitoring; and frame the questions that may eventually be explored through quantitative modeling efforts. The conceptual models will identify the key drivers/factors that need to be incorporated into models (e.g., internal processes of biogeochemical cycling of nutrients and carbon, including important internal sources and sinks, important physical drivers, and interactions between nutrients and other stressors). Because of the large differences in hydrography and nutrient dynamics between regions of the Bay, the Bay will be divided into a manageable number of segments and habitat-types, and conceptual models will be evaluated across these sub-embayments and habitat types. 

Task 2.2 Develop Problem statement and future scenarios

A problem statement will be developed for SFB that addresses the question “If SFB had a nutrient problem, how would it manifest itself?”  A nutrient problem can take multiple forms, and the form(s) may vary by subembayment and habitat, and seasonally. The problem statement will address this spatial and seasonal variability, and be linked to beneficial use impairment.

With the problem statement identifying states of the SFB ecosystem that would result in beneficial use impairment, and the conceptual models from Task 2.1 serving as a framework for evaluating change, a list of plausible future scenarios for the Bay will be developed that identify changes that could lead to a problem, and scenarios under which a problem would be less likely to occur.  Two broad categories of scenarios are envisioned: i) changes in management actions (e.g., increases or decreases in nutrient loads via various sources, changes in the timing or quantity of freshwater flows); and ii) changes in environmental factors outside of human control (e.g., changes in suspended sediment load and water clarity, changes in temperature, interannual variability in freshwater flow, large-scale climate forcings and climate change).

The combination of the conceptual models and evaluation of future scenarios will assist in visualizing the spectrum of current, suspected, or potential future sources of impairment.

Task 2.3 Synthesize and Interpret Existing Ambient Water Quality Data and Identify Major Data or Conceptual Gaps in Bay Response to Nutrients

This task will synthesize and interpret nutrient and phytoplankton-related data in SFB’s subembayments. The data will be interpreted within the context of the conceptual models developed in Task 2.1, and where necessary conceptual models will be modified to reflect new insights. Goals will include: i) identifying spatial, seasonal, and temporal trends in ecosystem condition or response; ii) developing improved understanding of ecosystem response to nutrients; and iii) compiling and preparing data for eventual use in numerical modeling.

Based on analysis in Tasks 2.1-2.2, this task will also identify major data and knowledge gaps, and identify monitoring priorities and additional scientific investigation (e.g., Special Studies) that will be required in order to adapt conceptual models into quantitative models (Work Element 6).

Task 2.4 Develop Nutrient Loading Conceptual Model

A conceptual model for external loads to SFB will be developed that considers major sources and pathways through the watershed, airshed, and oceanic sources. This conceptual model will identify differences in important loads between subembayments.

Task 2.5 Synthesize Existing Loading Data and Identify Data Gaps

The purpose of this task is to synthesize existing information to develop, to the extent possible, spatially and temporally explicit estimates of nutrient and organic carbon external loads via major pathways. This task will also identify major data gaps that contribute to current uncertainty in total loads, speciation of those loads, and the relative importance of various sources.

The Interagency Ecological Program’s (IEP) conceptual model for the Pelagic Organism Decline (POD) recognizes that multiple factors may be acting in concert to degrade habitat and contribute to the sudden decline in native and non-native pelagic fish species (Baxter et al., 2010) in Suisun Bay and in the Delta. Factors considered include physical alterations to habitat; water withdrawals and changes in flow regime; land use changes; invasive species (including the Asian overbite clam, Potamocorbula amurensis, and multiple invasive copepods and other zooplankton); and changes in nutrient concentrations. Recent studies have argued that anthropogenic nutrient loads, in particular ammonium (NH4), play a role in ecosystem change and degradation. Dugdale et al (2007, 2012) and Parker et al. (2012a,b) make the case that elevated NH4 concentrations in Suisun and the Delta inhibit primary productivity (Dugdale et al., 2007; Parker et al., 2012a,b), and potentially contribute to low phytoplankton biomass in Suisun, with cascading effects up the food web.  Elevated NH4 levels have been suggested to contribute to the increased frequency of Microcystis blooms in the Delta (Lehman et al., 2008). Changes in nutrient ratios (N:P) and forms of N have been hypothesized to be exerting additional bottom-up pressures on Delta and Suisun food webs, through influencing phytoplankton community composition and other pathways (e.g., Glibert et al., 2011).

Given the scientific and regulatory attention that issues such as elevated NH4 and shifts in N:P are receiving in Suisun Bay, and in order to resolve the differing scientific perspectives on the issues, a separate work element was created. Nutrient related issues can be divided into four broad categories: 1. NH4 inhibition of primary production; 2. NH4 toxicity to copepods (e.g., Teh et al., 2011); 3. NH4 concentration increases and N:P shifts, and effects on phytoplankton community composition and the Suisun/Delta food web; and 4. other potential causes of low primary productivity in Suisun. A detailed accounting of all relevant projects and their timelines is beyond the scope of this document, but is under development in Task 3.2.

Activities Update

Task 3.1 Field studies and experiments to assess potential impairment due to elevated ammonium or changes in N:P

A number of field and laboratory studies are underway, some affiliated with the Nutrient Strategy (e.g., Suisun/SWAMP link) or funded by the Delta Science Program or the State and Federal Contractors Water Agency (SFCWA).  Other studies are currently under review, or are funded and slated to start in late 2012 or 2013. These studies will be tracked, results synthesized (Task 3.2), and where applicable conceptual models will be refined to incorporate new understanding.

Task 3.2 Synthesis of Research to Date and Suisun Ambient Water Quality Data

A series of synthesis reports will be prepared related to 1. NH4 inhibition of primary production; 2. NH4 toxicity to copepods; and 3. NH4 concentration increases and N:P shifts, and effects on phytoplankton community composition and the Suisun/Delta food web.

These reports will summarize results of peer-reviewed studies or reports from Suisun and the Delta to date, as well as relevant studies from other systems. In addition to reviewing published work, new analyses and data interpretation will be carried out, utilizing the abundant monitoring data collected by IEP/DWR and USGS, with the goal of characterizing temporal and seasonal trends, quantifying loads and internal transformations of nutrients, and using statistical tools to identify potential causal mechanisms underlying ecosystem change.

Task 3.3 Assess Science Related to Ecosystem Impacts in Suisun Bay and Relationship to Nutrients

An approach is necessary to resolve issues that have been raised relative to nutrient impacts in Suisun Bay. The strategy recommended here is to convene one or more expert panels and sponsor technical workshops to address the three broad categories of proposed nutrient-related impairment in Suisun Bay. The goals of these expert panels will include: 1. Evaluating existing scientific evidence for nutrient-related impairment in Suisun Bay; 2. Identifying areas of agreement and disagreement within the scientific literature and among the regional research community; 3. Recommending studies that can address critical conceptual gaps and data gaps. The results of these panels and the reports from Task 3.2 will be used to refine conceptual models and inform monitoring and special studies (Work Element 5) and modeling (Work element 6).

The purpose of this work element is to develop the technical foundation for policy decisions to establish nutrient-related water quality objectives. This strategy assumes that the development of nutrient related water quality objectives would be accomplished using an approach consistent with the “nutrient numeric endpoint framework”—the numeric guidance that would serve as a means to translate narrative nutrient water quality objectives.  This numeric guidance will be centered on an "assessment framework," a structured set of indicators and associated thresholds that can be used to categorize potential ecological states of the Bay from supporting to impairment of beneficial uses. These assessment frameworks also specify the spatial and temporal density and types of data needed to make an assessment of beneficial uses support.

The Bay NNE literature review and data gaps analysis proposed a suite of indicators appropriate to assess the effects of eutrophication and other adverse effects of nutrients on Bay beneficial uses (McKee et al. 2011). Indicators were proposed for three principal habitat types: 1) subtidal unvegetated habitat, 2) vegetated subtidal (seagrass and other SAV), and 3) intertidal flats. The review proposes specific tasks to develop the NNE assessment framework for each habitat types. These tasks are given in Table 3. An initial rank of high, medium, and low priority was assigned to each by the Water Board. Prioritization of work elements reflects: 1) percentage of habitat type represented in the Bay and 2) best professional judgment as to whether an indicator represents the most sensitive assessment of potential impacts to beneficial uses. Based on these two criteria, phytoplankton (biomass and community composition), dissolved oxygen, HABs and HAB toxins were the primary NNE indicators of interest in unvegetated subtidal habitat. Ammonium, N:P ratio and other nutrient forms are also indicators of interest, pending the outcome of studies being conducted in Suisun Bay (see Work Element 3) and assessment by a working group of scientists.

Indicators representative of other habitat types such as intertidal flats and seagrass are of high interest in the Bay as well as other estuaries around the state.  Several studies are ongoing to support decisions on NNE thresholds in California estuaries outside of the Bay. Thus, these work elements are designated as moderate priority, with the intention of evaluating the applicability of these studies to assessment of these habitats in San Francisco Bay sometime in the future.,

Five tasks were designated as high priority and as such they are components of planned activities during the first four years.  

Activities Update

Task 4.1 Nutrient  Assessment Framework

The purpose of this task is to develop an assessment framework that considers the use of phytoplankton and nutrient forms (e.g. ammonium and other nutrient species or ratios) to assess the condition of the Bay.  This will be done by choosing the precise indicators and metrics; specifying how and when they will be measured; and creating decision rules for how the indicators will be combined in order to classify Bay segments into categories of degree of beneficial use support (from supporting to impairing beneficial uses).  Existing data on phytoplankton, nutrients and other co-factors will be used to graphically illustrate options with respect to how to use data to make an assessment. Where feasible, results from model simulations will be used to inform assessment framework development (e.g, linkages between phytoplankton biomass and low dissolved oxygen). 

The influence of ammonium on the magnitude of primary productivity as well as the composition of phytoplankton community in different regions in the Bay is a topic of intense interest and research in the Bay. This ongoing research must be synthesized to develop a fuller perspective on the need for concentration-based objectives for ammonium.  As such, work under Task 4.1 will be carried out in close coordination with Work Element 3, and may also be informed by the use of biogeochemical models in Task 6.2.a to assess the relative importance of ammonium’s inhibitory role in primary production. In addition, this Task 4.1 will coordinate with efforts in Task 3.3 to identify data gaps or studies that may still need to be conducted to determine the need for and approach to next steps with respect to incorporating ammonium into the NNE assessment framework for the Bay.

Task 4.2. Review of Dissolved Oxygen Objectives

McKee et al. (2011) found that dissolved oxygen monitoring data taken along the longitudinal "spine" of the SF Bay typically meets established DO objectives. However, SF Bay dissolved oxygen objectives were established in the first Basin Plan in 1975 and the science of supporting derivation of dissolved oxygen objectives has evolved considerably since that time. The main focus of this review is on the application of the DO objectives to shallow water habitats, tidal marshes, managed ponds and tidal sloughs, although it can be argued that a comprehensive review should be conducted. Near-term tasks consist of: 1) synthesizing existing dissolved oxygen data; and 2) evaluating the adequacy of existing dissolved oxygen objectives. 

4.2.a Synthesize existing dissolved oxygen data

This task will synthesize existing dissolved oxygen data Bay-wide and for specific habitats, such as tidal sloughs, and shallow subtidal areas. This topic was not covered in the Bay NNE literature review and data gaps analysis (McKee et al. 2011). The synthesis effort will include analysis of data currently being collected (since 2011) at 6 USGS moored stations (DO, chlorophyll, and fluorescence), as well as other data sources, including historical studies conducted in the Lower South Bay. This synthesis will assess status and trends of dissolved oxygen relative to Basin plan standards, and will assess whether objectives are being met and whether there is evidence of impairment.

4.2.b Evaluate the adequacy of the dissolved oxygen objectives and the need for site specific objectives 

The purpose of this task is to synthesize data on dissolved oxygen requirements of species representing the variety of beneficial uses in SF Bay and to inform whether there is a need to revise dissolved oxygen objectives for SF Bay.  The product would be a report that synthesizes methodology, summarizes availability of DO tolerance data for key indicator species, and, assuming data are available, calculates DO criteria protective under acute and chronic conditions for the range of beneficial uses represented in SF Bay. To the extent feasible, this analysis will also qualitatively consider naturally occurring low oxygen (e.g., in tidal wetlands or in waters exiting naturally low-oxygen habitats) versus low oxygen due to anthropogenic perturbations. Depending on available resources, this work may be phased so that shallow subtidal areas and tidal sloughs are initially the focus of the review. Based on the synthesis in subtask 4.2b, data gaps will be identified and, if necessary, recommendations for additional data collection to support the derivation of DO criteria will be made.

Task 4.3. Macroalgal NNE Assessment Framework. 

The objectives of this task are: 1) to document baseline abundance of macroalgae in a variety of habitat types and regions of the Bay and 2) participate in statewide effort to develop an assessment framework for eutrophication in intertidal flats and shallow subtidal habitat, based on macroalgae. The intent is that progress on this work element would be monitored for applicability to the Bay and that SF Bay stakeholders have the opportunity to comment on studies supporting these work elements, while progress is made on other tasks. 

The purpose of this work element is to develop the San Francisco Bay monitoring program.  Targeted habitats include unvegetated and vegetated subtidal and mudflat habitat in the Bay. Managed pond habitats will be excluded, as this habitat type will be addressed in a separate work element in the strategy.  Two major tasks are associated with this work element.

Activities Update

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Task 5.1. Develop a Monitoring  Program:

5.1.a Identify elements of a core SF Bay monitoring program to assess status and trends of loads and Bay response.

The purpose of this task is to recommend specific indicators and methods, spatial and temporal density of sampling that should be included in a “core” monitoring program to make regular assessments of the status of the Bay with response indicators and to assess trends in external nutrient loads and response. An evaluation of existing monitoring activities in the Bay will be considered, along with the potential for maximizing synergies and leveraging resources. The product of Task 5.1.a. will be used to develop a detailed nutrient monitoring program for the Bay (5.1.c). Load monitoring may be included as an element of the monitoring program for point and non-point sources, including stormwater, wastewater, agriculture and Delta inputs to the northern estuary.

5.1.b Develop a program of special studies to improve fundamental understanding and quantification of processes in the system

In addition to status and trend monitoring, special studies will be carried out to address fundamental data or conceptual gaps that need to be filled to support the assessment framework and model calibration and validation. Data or conceptual gaps identified in Tasks 2.3, 2.5, 3.2, 3.3,  4.1, 4.2, 6.2b, and 6.3 will be compiled and prioritized within Task 5.1.b

5.1.c Develop San Francisco Bay nutrient monitoring program Work Plan and QAPP. 

The purpose of this work element is to develop the work plan and quality assurance project plan (QAPP) for the Bay nutrient monitoring program. The work plan and QAPP covers monitoring to assess status and trends in external nutrient loads and ecosystem response of the Bay to those loads. This task includes development of field, sampling handling, laboratory analyses, data management and reporting procedures for data collection.

Task 5.2 Implement the San Francisco Bay nutrient monitoring program. 

The purpose of this work element is develop models to forecast the nutrient and carbon sources, pathways, and loads to SF Bay and simulate the ecological response to those loads and other environmental factors in the Bay.  These models will be used to engage stakeholders in discussion of options for nutrient management under a variety of different scenarios. Previous work elements will define conceptual models and scenarios of interest (Work Element 1), and management endpoints of concern (Work Element 2).

Activities Update

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Task 6.1. Modeling of External Sources

Task 6.1.a Basic Loading Estimates or Modeling

Building on the loading conceptual model and loading data compiled in Tasks 2.3 and 2.4, respectively, initial nutrient load estimates will be calculated. To the extent feasible, spatially explicit (e.g., subembayments) and temporally-explicit nutrient loads will be quantified.  The nutrient sources considered will include: POTW discharges; stormwater discharges; flows from the San Joaquin and Sacramento Rivers entering through the Delta, along with other smaller downstream tributaries; exchange across the Golden Gate; and direct atmospheric deposition.  Nutrient fluxes from Bay sediments to the water column will also be considered. Initial estimates of POTW loads will be based on treatment technologies employed (expected effluent nutrient speciation and concentrations) and flow.  When historical data is available, these data will be used to refine POTW loads.  In addition, the Water Board is requiring a two year effluent characterization data collection effort (July 2012 through 2014) by Bay area municipal wastewater dischargers and industrial dischargers. These data will be used to further refine load estimates.

Task 6.1.b Review models for Estimating Nutrient/ Organic Carbon Loads

This task will review existing models or types of models that can be used to estimate the sources and pathways of nutrient load to the Bay and summarize the data requirements. The task will begin by identifying the types of questions that the model(s) or empirical data must answer.  The intent is to review models and tools that can assist in decision-making on nutrient management strategies and test the cost-effectiveness of implementation scenarios.  This work element will feed into the development of a modeling strategy.

Task 6.2. Modeling of Load-response

Task 6.2.a. Basic Numeric Modeling and Scenario Analysis

The purpose of this task is to develop and apply basic numeric biogeochemical models, as an early step in modeling efforts, to inform future model development and data collection. The models will be used to quantitatively synthesize existing data; develop nutrient budgets; support evaluation of proposed indicators as part of the NNE; test appropriate management endpoints; determine how key processes should be modeled and assess the relative importance of and uncertainty related to those processes; and identify major data gaps at an early stage to inform the monitoring program and the need for special studies. In addition, these models may be used to evaluate biological responses under future scenarios (e.g., changes in nutrient loads, changes in major physical drivers affecting productivity, decreases in suspended sediment concentrations).

Initial model development will focus on Suisun Bay and South Bay or Lower South Bay.  A technical advisory group consisting of regional and national experts would be convened to develop a modeling study plan. A key task of this group will be to identify the main questions to be addressed through the modeling work, approaches for incorporating key processes into the model, and the appropriate model platform(s). It should be emphasized that the model(s) developed and used in this task are not intended to be the final models that may ultimately be required for the Bay (which may be more complex and computationally intensive), but rather as scoping tools.

Task 6.2.b. Review of existing models and available model approaches to model the ecological response of the Bay to nutrient loads and other co-factors.

This task will produce a review of available models and/or modeling platforms that will be the basis for developing a modeling strategy for the Bay. A work group will identify the management questions and endpoints (indicators) of concern and relevant spatial and temporal scales, focusing on hydrodynamic, water quality (dissolved oxygen, nutrients, carbon) and a phytoplankton-zooplankton production and phytoplankton speciation models. A review will be conducted of existing Bay and Delta hydrodynamic and water quality models or other applicable types of models, from simple spreadsheet to complex dynamic simulation models, their data needs, and advantages and disadvantages.

Task 6.3. Develop and Implement Modeling Strategy

The purpose of this task is to synthesize information generated from Tasks 6.1 and 6.2 tasks to develop a modeling strategy for the Bay. The strategy will identify questions to be answered by the models and what policies will be informed; types of models needed (e.g. external loads, bay hydrodynamic and water quality); potential modeling platforms; amount of data required and estimates of cost; and schedule. Information will be presented as cost/benefits of model options with trade-offs in terms of what indicators can be modeled at varying levels of accuracy/precision or timescales.  The strategy will also address what partnerships need to be created to build and maintain a model.

This work element will identify control strategies that are feasible in the near-term and long-term for reducing nutrient loads to the Bay, and evaluate their potential effectiveness for addressing nutrient-related impairment in the Bay, and their cost-efficiency. A work group will be convened to identify key decisions and environmental, technical, and economic considerations, and develop work plans and scopes of work. All major nutrient sources will be considered, including POTW loads, stormwater runoff, and agricultural and other loads from the Delta. Effort directed toward exploring control strategies for various sources will be prioritized based on their relative importance and potential for load reductions, and based on spatial/temporal considerations.  The evaluation of control strategy options will also consider multiple benefits. Work Element 7 will be carried out in parallel with the other activities above so that implementation plan scenarios can be considered once proposed nutrient objectives are developed.  Where applicable, implementation scenarios will be evaluated and refined through modeling work in Task 6.4.  Where necessary and feasible, the potential effectiveness of control strategies will be evaluated through scenario modeling (Task 6.3). 

Table 2. GANTT chart of approximate timing of work elements and tasks associated with 5-yr nutrient plan. 

Table 3. Specific recommendations for science to support development of habitat-type specific NNE assessment frameworks.