Dissolved inorganic nitrogen (DIN) and phosphorus (DIP) are essential nutrients for primary production that supports estuarine food webs. However DIN and DIP concentrations in San Francisco Bay (SFB) greatly exceed those in other US estuaries where water quality has been impaired by nutrient pollution. SFB receives high nutrient loads from treated wastewater effluent, agricultural runoff, and stormwater.SFB has long been recognized as a nutrient-enriched estuary, but one that has exhibited resistance to some of the classic symptoms of nutrient overenrichment, such as high phytoplankton biomass and low dissolved oxygen. SFB receives high nutrient loads from treated wastewater effluent, agricultural runoff, and stormwater. Research and monitoring in SFB over the last 40 years have identified several factors that have historically imparted resistance to the adverse effects of high nutrient loads: high turbidity, strong tidal mixing, and abundant filter-feeding clam populations, all of which tend to limit the efficiency with which DIN and DIP are converted into phytoplankton biomass. While these factors have arguably had a protective effect in many areas of SFB with respect to nutrients, they have negatively impacted the northern estuary by severely limiting food web productivity there.

However, recent observations indicate that SFB’s resistance to high nutrient loads may be weakening. These observations include: a 3-fold increase in summer-fall phytoplankton biomass in South Bay since 1999; frequent detections of algal species that have been shown in other nutrient-rich estuaries to form harmful blooms; frequent detection of the toxins microcystin and domoic acid that are produced by some types of algae; an unprecedented red tide bloom in Fall 2004; low dissolved oxygen in some margin habitats, including sloughs and salt ponds; and studies suggesting that the chemical forms of nitrogen can decrease phytoplankton productivity or alter their community composition. To address growing concerns that SFB’s response to nutrients is changing, the San Francisco Bay Regional Water Quality Control Board worked collaboratively with stakeholders to develop the San Francisco Bay Nutrient Management Strategy (NMS), which lays out an overall approach for building the scientific understanding to support well-informed nutrient management
decisions. 

Among its early priorities, the NMS recognized the need for a conceptual model to lay the scientific foundation to guide the NMS’ implementation. This report targets that need and aims to achieve four main goals:

1. Develop conceptual models connecting nutrient loads and cycling with ecosystem response in SFB;
2. Apply those conceptual models to identify scenarios under which nutrient-related impairment may occur in SFB’s subembayments; and
3. Identify knowledge and data gaps that need to be addressed in order for well-informed, science-based decisions to be made about how best to manage nutrient loads to mitigate or prevent adverse impacts.
4. Develop an approach to prioritizing among data and knowledge gaps, and apply that approach to generate an initial recommended set of highest priority activities to inform the development of a science plan to guide NMS implementation.

This report was developed in collaboration with a team of regional scientists whose areas of expertise cover a range of relevant disciplines (see Table 1.1). Its main observations and recommendations are:

1. Changes in SFB’s response to nutrient loads over the past decade, combined with the Bay’s high nutrient loads and concentrations, justify growing concerns about elevated nutrients.
2. The future trajectory of SFB’s response to nutrients is uncertain. One plausible trajectory is that SFB maintains its current level of resistance to the classic effects of high nutrient loads and no further degradation occurs. A second, equally plausible scenario is that SFB’s resistance to nutrients continues to decline until adverse impacts become evident. The highly elevated DIN and DIP concentrations Bay-wide provide the potential for future impairment. Any major reductions in loads to SFB will take years-to-decades to implement. Thus, if future problems are to be averted, potential impairment scenarios need to be anticipated, evaluated, and, if deemed necessary, managed in advance of their onset.
3. By considering current conditions in SFB, trends of changing ecosystem response, and a conceptual model for SFB’s response to nutrients, we identified the following highest priority issues:
   1. Determine whether increasing biomass signals future impairment. This issue is most pertinent for Lower South Bay and South Bay.
   2. Characterize/quantify the extent to which excess nutrients contribute now, or may contribute in the future, to the occurrence of HABs/NABs and phycotoxins.
   3. Determine if low DO in shallow habitats causes adverse impacts, and quantify the contribution of excess nutrients to that condition.
   4. Further evaluate other hypotheses for nutrient-related adverse impacts to ecosystem health, including nutrient-induced changes in phytoplankton community composition and ammonium inhibition of primary production. That evaluation – to include data analysis, additional experimentation, or modeling – should assess their potential quantitative importance, and help to determine if they should be considered among the highest priority issues.
   5. Test future scenarios that may lead to worsening conditions through the use of numerical models.
   6. Quantify the contributions of nutrients by sources in different areas of the Bay, considering both their transport and in situ transformations and losses.
   7. Evaluate the potential effectiveness of various nutrient management strategies at mitigating or preventing adverse impacts.
4. Although concern related to changing ecosystem response in SFB is warranted, widespread and severe nutrient-related impacts do not currently appear to be occurring, based on existing sampling locations and parameters commonly measured. This apparent lack of current severe impacts translates into time for conducting investigations to improve understanding of SFB’s response to nutrients and allows for sound, science-based management plans to be developed and implemented. That said, the considerable amount of time required to implement any management strategy raises the level of urgency such that work should move forward expeditiously.
5. Given the stakes of no action - and the time required for data collection, analysis, and modeling tools to reach a useable state - work needs to move forward in parallel on implementing multiple aspects of the Nutrient Strategy. A well-coordinated program is needed to maximize the effectiveness and efficiency of this effort. That program needs to integrate seamlessly across what
   might otherwise be (or become) semi-independent program areas. Specifically, we recommend the following set of highly-integrated program areas:
   1. Monitoring: Develop and implement a sustainably-funded and regionally administered monitoring program that continues routine monitoring, and fills newly-identified data gaps relevant to nutrients;
   2. Modeling: Develop and apply linked hydrodynamic and water quality models to integrate observations, identify critical data gaps (to be addressed through monitoring or experimental studies), quantify processes at the ecosystem scale, and evaluate future scenarios (including management alternatives);
   3. Observational and Experimental Studies: Undertake special studies (field investigations, controlled experiments) to address the highest priority knowledge and data gaps identified in #3; and
   4. Data Synthesis and Interpretation: Analysis of existing and newly collected data (from monitoring and experimental studies), incorporating models, to improve understanding of linkages between nutrients and ecosystem response and to inform the development of an assessment framework.
6. The Delta/Suisun boundary, while an important regulatory boundary, is not meaningful from ecological and loading standpoints. Nutrient loads to and transformations within the Delta exert considerable influence over nutrient loads to and ambient concentrations within Suisun, San Pablo, and Central Bays. Furthermore, the ecology and habitat quality of the Delta and Suisun Bay are tightly coupled. A unified approach – one that spans the Bay-Delta continuum - for evaluating the impacts of nutrients on beneficial uses will best serve both ecosystem health in the Bay-Delta and the information needs of environmental managers.

The report is lengthy, but the majority of its length comes from sections devoted to the development of a detailed conceptual model (Sections 5-9). For a higher-level read that still covers the key issues, main findings, and recommendations, we suggest reading the following sections:

• Sections 1-2: brief description of report goals and approach, and background on the NMS.
• Section 3: Overview of current conditions and a description of how nutrient-related problems would be expected to manifest in San Francisco Bay
• Section 4: Brief description of the conceptual model structure/approach
• Section 11: Identifying highest the priority scenarios, science questions, and data/knowledge gaps
• Section 12: Summary of main observations and recommendations