Nutrient Management Strategy Science Plan Report

San Francisco Estuary Institute (SFEI) | September 9th, 2016

The San Francisco Bay (SFB) estuary receives large inputs of the nutrients nitrogen and phosphorous from anthropogenic sources, and has the potential to suffer negative

The San Francisco Bay (SFB) estuary receives large inputs of the nutrients nitrogen and phosphorous from anthropogenic sources, and has the potential to suffer negative impacts from nutrient overenrichment. Nutrient concentrations in SFB exceed those in other estuarine ecosystems where degradation is strongly expressed. To date, SFB has shown resistance to some of the classic symptoms of nutrient over-enrichment, such as excessive phytoplankton biomass as chlorophyll-a (chl-a) and low dissolved oxygen (DO). Recent observations, however, suggest that SFB’s resistance to nutrient enrichment is weakening, and have generated concern that SFB may be trending toward, or may already be experiencing, adverse impacts due to its high nutrient loads. In response to these concerns, the San Francisco Bay Regional Water Quality Control Board (SFBRWQCB) worked collaboratively with stakeholders to develop the San Francisco Bay Nutrient Management Strategy (NMS).1 The NMS lays out an overall approach for developing the underlying science to support nutrient management decisions. This report presents a Draft Science Plan for implementing the SFB NMS. The report’s main goals include: Lay out a multi-year Science Plan representing a logical sequence of studies to inform major management decisions, assuming a time-line of 10+ years. Develop an approach and rationale for sequencing and prioritizing among studies, and identify specific high-priority studies, in particular those that should proceed in FY2016- 2018. Provide realistic estimates of the time-frame and funding needed to support a Science Plan that will successfully inform management decisions. The Draft Science Plan was developed in 2014-15 with input from science advisors (Table 1.1), the NMS Steering Committee, and the NMS Nutrient Technical Work Group (Fig. 1.1). Projects are described in more detail in the first 1-3 years, and in increasingly less detail over time, recognizing that the Science Plan will be iteratively refined based on new insights gained as work progresses.

Nutrient Management Strategy Science Program

San Francisco Estuary Institute (SFEI) | September 1st, 2017

San Francisco Bay (SFB) receives large inputs of the nutrients nitrogen (N) and phosphorous (P) from anthropogenic sources. N and P are essential components of a healthy

San Francisco Bay (SFB) receives large inputs of the nutrients nitrogen (N) and phosphorous (P) from anthropogenic sources. N and P are essential components of a healthy estuary, supporting primary production at the base of the food web. However, ambient N and P concentrations in SFB exceed those in many other estuarine ecosystems, including those considered eutrophic1 and that experience nutrient-related impairment, such as excessive phytoplankton blooms and prolonged periods of low dissolved oxygen (DO). Unlike those other nutrient-enriched estuaries, though, SFB has exhibited resistance to classic eutrophication symptoms. Recent observations, however, suggest that SFB’s resistance to nutrient enrichment is weakening (e.g., Cloern et al., 2007; Cloern et al., 2010; SFEI 2014a).  These San Francisco Bay Nutrient Management Strategy (NMS) Science Program was launched in 2014 to develop the scientific foundation to support nutrient management decisions. The NMS Steering Committee, representing 13 stakeholder groups (regulators, dischargers, water purveyors, NGOs, resource agencies) oversees the NMS’ implementation, including financial oversight and alignment of NMS science activities with high priority management questions. The San Francisco Estuary Institute (SFEI) serves as the technical lead on implementing the NMS Science Program. SFEI staff work with regional collaborators to carry out NMS projects, including field investigations, monitoring, and data interpretation. 

Opportunities to Accelerate Nature-Based Solutions: A Roadmap for Climate Progress, Thriving Nature, Equity, and Prosperity

White House Domestic Climate Policy Office | November 30th, 2022

Optimizing the dammed: Water supply losses and fish habitat gains from dam removal in California

Journal of Environmental Management (Elsevier) | April 1st, 2014

Dams provide water supply, flood protection, and hydropower generation benefits, but also harm native species by altering the natural flow regime and degrading aquatic an

Dams provide water supply, flood protection, and hydropower generation benefits, but also harm native species by altering the natural flow regime and degrading aquatic and riparian habitat. Restoring some rivers reaches to free-flowing conditions may restore substantial environmental benefits, but at some economic cost. This study uses a systems analysis approach to preliminarily evaluate removing rim dams in California's Central Valley to highlight promising habitat and unpromising economic use tradeoffs for water supply and hydropower. CALVIN, an economic-engineering optimization model, is used to evaluate water storage and scarcity from removing dams. A warm and dry climate model for a 30-year period centered at 2085, and a population growth scenario for year 2050 water demands represent future conditions. Tradeoffs between hydropower generation and water scarcity to urban, agricultural, and instream flow requirements were compared with additional river kilometers of habitat accessible to anadromous fish species following dam removal. Results show that existing infrastructure is most beneficial if operated as a system (ignoring many current institutional constraints). Removing all rim dams is not beneficial for California, but a subset of existing dams are potentially promising candidates for removal from an optimized water supply and free-flowing river perspective. Removing individual dams decreases statewide delivered water by 0–2282 million cubic meters and provides access to 0 to 3200 km of salmonid habitat upstream of dams. The method described here can help prioritize dam removal, although more detailed, project-specific studies also are needed. Similarly, improving environmental protection can come at substantially lower economic cost, when evaluated and operated as a system.

Patterns and magnitude of flow alteration in California, USA

Freshwater Biology (Wiley) | December 27th, 2017

The importance of the natural flow regime to stream and river health has received growing attention over the last two decades. Quantifying natural river flows has become

The importance of the natural flow regime to stream and river health has received growing attention over the last two decades. Quantifying natural river flows has become an essential component of water resource planning, including assessments of water supplies (Vicuna,Maurer, Joyce, Dracup, & Purkey, 2007; Wurbs, 2005), reservoir operations (Hejazi, Cai, & Ruddell, 2008) and drought risk (Meko,Therrell, Baisan, & Hughes, 2001). Understanding the natural flow regime is also crucial for managing stream ecosystems.

Paying it Forward: The Path Toward Climate-Safe Infrastructure in California

Climate-Safe Infrastructure Working Group | September 1st, 2018

Pollutants of concern (POC) reconnaissance monitoring final progress report, water year (WY) 2015

San Francisco Estuary Institute (SFEI) | June 6th, 2016

The San Francisco Bay mercury and PCB TMDLs called for implementation of control measures to reduce PCB and mercury loads entering the Bay via stormwater. Subsequently,

The San Francisco Bay mercury and PCB TMDLs called for implementation of control measures to reduce PCB and mercury loads entering the Bay via stormwater. Subsequently, the San Francisco Bay Regional Water Quality Control Board (Regional Water Board) issued the first combined Municipal Regional Stormwater Permit (MRP). This first MRP contained provisions aimed at improving information on stormwater pollutant loads in selected watersheds (Provision C.8.) and piloted a number of management techniques to reduce PCB and Hg loading entering the Bay from smaller urbanized tributaries (Provisions C.11. and C.12.). In November 2015, the Regional Water Board issued the second MRP. “MRP 2.0” places an increased focus on finding watersheds, sources areas, and source properties that are potentially more polluted and are therefore more likely to be cost effective areas for addressing load reduction requirements through implementation of control measures. To support this increased focus, a stormwater characterization monitoring program was developed and implemented beginning in Water Year (WY) 2015. This same design is being implemented in the winter of WY 2016 by the RMP, the San Mateo Countywide Water Pollution Prevention Program and the Santa Clara Valley Urban Runoff Pollution Prevention Program. In addition, the RMP is piloting a project to explore the use of alternative un-manned “remote” suspended sediment samplers. During WY 2015, composite stormwater samples were collected from 20 watershed locations. At three of these locations, data were also collected using two remote suspended sediment sampler devices, both of which are designed to enhance settling and capture of suspended sediment particles from the water column. This report summarizes and provides a preliminary interpretation of data collected during WY 2015. The data collected is contributing to a broader effort to identify potential management areas. The report is designed to be updated in subsequent years as more data are collected.

Preparing Scientists, Policy-Makers, and Managers for a Fast-Forward Future

University of California, Davis (UC Davis) | June 15th, 2021

Primary Production in the Sacramento-San Joaquin Delta: A Science Strategy to Quantify Change and Identify Future Potential

San Francisco Estuary Institute (SFEI) | May 20th, 2019

Today’s Sacramento-San Joaquin Delta is an unusually low-productivity estuary. The constraints on primary production and the relative importance of different production

Today’s Sacramento-San Joaquin Delta is an unusually low-productivity estuary. The constraints on primary production and the relative importance of different production sources to the food web are major ecological uncertainties in the Delta system. Understanding how the extensive historical changes in the Delta landscape have altered primary production has the potential to inform restoration planning and management across the region.  The Delta Landscapes Project (SFEI-ASC 2014) has recently produced information that allows us, for the first time, to answer questions about historical primary production and carrying capacity from quantified changes in the areal extent and spatial configuration of habitat types in the Delta since the mid-19th century. Our focus is on estimating primary production because the potential capacity of ecosystems to support fish, bird and other wildlife populations is set by primary production – the supply of food required to produce animal biomass. 

Priorities for California’s Water: Advancing Research During Uncertain Times

Public Policy Institute of California (PPIC) | November 12th, 2025

In California, research underpins all water-related activity. It is vital for coping with too much water, too little water, and rapid changes in hydrology. Whether you ar

In California, research underpins all water-related activity. It is vital for coping with too much water, too little water, and rapid changes in hydrology. Whether you are a farmer managing the precise application of water to your crops, a utility providing clean drinking water supplies to your community, or a restorationist trying to heal a damaged wetland, your actions rely upon decades of applied research that guides your actions and measures your success.  The same reliance on research applies if you are developing policies to reduce the price of water, increase its reliability, regulate its usage, and reduce hazards from floods. None of this works without a vast research enterprise that is regularly updating the science and technology we use to manage water, prepare for the future, inform the public, and address new problems as they arise.