Pilot Study Examining Spatial Differences in Water Quality Between Shoal and Channel Habitats

San Francisco Estuary Institute (SFEI) | August 1st, 2019

Under the umbrella of the Nutrient Management Strategy (NMS; www.sfbaynutrients.sfei.org), we are investigating relationships between the SFB’s elevated nutrient levels

Under the umbrella of the Nutrient Management Strategy (NMS; www.sfbaynutrients.sfei.org), we are investigating relationships between the SFB’s elevated nutrient levels and phytoplankton production, with the goal of identifying protective nutrient loads and effective nutrient management options. To address these goals, NMS work includes continued ship-based monitoring (in collaboration with USGS); augmenting that monitoring with high-frequency sensor data and intensive field studies; and developing coupled hydrodynamic-biogeochemical models -- calibrated using field observations -- to simulate water quality under a range of forcings.

Pilot Study of Contaminants of Emerging Concern (CECs) in the Russian River Watershed: Lessons Learned

San Francisco Estuary Institute (SFEI) | December 21st, 2017

Contaminants of emerging concern (CECs) can be defined as any chemicals that are not regulated or commonly monitored but have the potential to enter the environment and c

Contaminants of emerging concern (CECs) can be defined as any chemicals that are not regulated or commonly monitored but have the potential to enter the environment and cause adverse ecological or human health impacts. Determining which of the thousands of chemicals in commerce are CECs and whether or not they may be a problem is a formidable challenge. For most chemicals in use, a number of limitations prevent researchers from measuring their presence and assessing their potential risks. It is therefore difficult to monitor and manage CECs.  In response, scientists and managers recently completed a Pilot Study Design1 for monitoring CECs in aquatic ecosystems throughout California. The Russian River watershed (RRW) study was the first regional implementation of this Pilot Study Design. The collected data provide useful information for both the Russian River region and the implementation of the monitoring framework in other areas.  The primary objective of this study was to investigate the occurrence of high priority CECs in receiving water, sediment, and fish tissue within the RRW to address the management question: 

Plan of Development Sacramento-San Joaquin Delta

Interagency Delta Committee (IDC) | January 20th, 1965

Policy for Maintaining Instream Flows in Northern California Streams

California State Water Resources Control Board (SWRCB) | September 28th, 2010

The State Water Resources Control Board (State Water Board or Board) adopted this state policy for water quality control on May 4, 2010. This policy is also known as the

The State Water Resources Control Board (State Water Board or Board) adopted this state policy for water quality control on May 4, 2010. This policy is also known as the North Coast Instream Flow Policy. It applies to applications to appropriate water, small domestic use and livestock stockpond registrations, and water right petitions. Water Code section 1259.4, which was added by Assembly Bill 2121 (Stats. 2004, ch. 943, § 3), requires the State Water Board to adopt principles and guidelines for maintaining instream flows in northern California coastal streams as part of state policy for water quality control, for the purposes of water right administration. This policy implements Water Code section 1259.4. The geographic scope of this policy, referred to as the policy area, extends to five counties—Marin, Sonoma, and portions of Napa, Mendocino, and Humboldt counties— and encompasses (1) coastal streams from the Mattole River (originating in Humboldt County) to San Francisco, and (2) coastal streams entering northern San Pablo Bay. This policy focuses on measures that protect native fish populations, with a particular focus on anadromous salmonids (e.g., steelhead trout, coho salmon, and chinook salmon) and their habitat. Beginning in 1996, the National Marine Fisheries Services (NMFS) and the California Department of Fish and Game (DFG) listed steelhead trout, coho salmon, and chinook salmon as “threatened” under the federal Endangered Species Act (ESA) and the California Endangered Species Act (CESA), respectively. In 2005, the coho salmon’s status was upgraded from threatened to “endangered” on both the ESA and the CESA lists. This policy establishes principles and guidelines for maintaining instream flows for the protection of fishery resources. It does not specify the terms and conditions that will be incorporated into water right permits, licenses, and registrations. It prescribes protective measures regarding the season of diversion, minimum bypass flow, and maximum cumulative diversion. Applicants may choose to implement the policy principles through the regionally protective criteria or site-specific studies. Site-specific studies may be conducted to develop alternative site-specific protective criteria. The policy also limits construction of new onstream dams and contains measures to ensure that approval of new onstream dams does not adversely affect instream flows needed for fishery resources. The policy provides for a watershed-based approach to evaluate the effects of multiple diversions on instream flows within a watershed as an alternative to evaluating water diversion projects on an individual basis. Enforcement requirements contained in this policy include a framework for compliance assurance, prioritization of enforcement cases, and descriptions of enforcement actions. The policy contains guidelines for evaluating whether a proposed water diversion, in combination with existing diversions in a watershed, may affect instream flows needed for the protection of fishery resources.

Preface to the Environmental Assessment for 2019 Ocean Salmon Fisheries Management Measures

National Marine Fisheries Service (NMFS) | April 1st, 2019

Preseason Report I Stock Abundance Analysis and Environmental Assessment Part 1 for 2019 Ocean Salmon Fishery Regulations (PRE I)

Pacific Fishery Management Council | March 1st, 2019

Primary Production in the Delta: Then and Now

University of California, Davis (UC Davis) | October 3rd, 2016

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by large-scale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how large-scale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach—based on ecosystem function—to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.

Projected Effects of Future Climates on Freshwater Fishes of California

California Energy Commission (CEC) | July 31st, 2012

A methodology is presented that allows systematic evaluation of climate change impacts on freshwater fishes in California (121 native fish taxa and 43 aliens). The method

A methodology is presented that allows systematic evaluation of climate change impacts on freshwater fishes in California (121 native fish taxa and 43 aliens). The methodology uses expert opinions of the authors and literature reviews of status and biology of the fishes to score both status of each species (“baseline vulnerability”) and likely impact of climate change (“climate change vulnerability”). Baseline and climate change vulnerability scores were highly correlated with one another and were consistent among different scorers. Native species were found to have both greater baseline and greater climate change vulnerability than alien species. Fifty percent of natives had critical or high baseline vulnerability versus none for aliens; 83 percent had critical or high climate change vulnerability versus 19 percent for aliens. Fishes with high baseline vulnerability were also likely to have highest vulnerability to climate change. These results show that predicted climate change effects on fresh water environments will dramatically change the fish fauna at all scales and at all elevations. The research team concluded that most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction, if present trends continue. Fishes requiring cold water (<22°C [72°F]) are particularly likely to go extinct. In contrast, most alien fishes will thrive, with many species likely to increase in abundance and range. However, even many aliens will ultimately be negatively affected through loss of aquatic habitats during severe droughts and stressful conditions in most waterways during summer months. On a regional scale (e.g., San Francisco Bay tributaries), vulnerability patterns follow statewide patterns and indicate the need for conservation strategies adapted to local conditions. Studies of three streams with long-term data on fish abundance indicate that native and alien species respond in different ways to variability in stream flow, which is likely to become more variable with climate change.

Prototyping structured decision making for water resource management in the San Francisco Bay-Delta

Environmental Science & Policy (Elsevier) | May 2nd, 2024

A structured decision making (SDM) approach can help evaluate tradeoffs between conservation and human-benefit objectives by fostering communication and knowledge transfe

A structured decision making (SDM) approach can help evaluate tradeoffs between conservation and human-benefit objectives by fostering communication and knowledge transfer among stakeholders, decision makers, and the public. However, the process is iterative and completing the full process may take years. It can be difficult to initiate an SDM effort when problems seem insurmountable. Occasionally, SDM may not even be the best or correct approach for addressing the conservation problem at hand. We describe the implementation of an SDM process to help inform difficult decisions related to competing objectives. We convened a diverse stakeholder group from the largest estuary in the western United States; the San Francisco Bay and Sacramento-San Joaquin Delta (Bay-Delta). The stakeholder group consisted of representatives from local, state, and federal agencies, non-profit organizations, and recreational fishers. The stakeholder group agreed on a problem statement and identified four priority objectives related to Chinook salmon, delta smelt, water availability and reliability, and agricultural water use. Furthermore, they proposed 14 candidate management actions to achieve their objectives. The group then used existing quantitative models and data to evaluate trade-offs in proposed management actions to identify areas of agreement of proposed candidate actions. The clear communication of the problem statement and objectives among the stakeholder group, along with evaluation of tradeoffs and uncertainty via decision-support models suggest that a full SDM approach may work in the Bay-Delta. We further communicate lessons learned during our implementation of SDM to help guide future SDM efforts in the region and elsewhere. See also: Structured Decision Making Delta Stewardship Council June 2024 meeting report.

Putting People over Fish: Stopping Radical Environmentalism to Provide Water to Southern California

The White House | January 20th, 2025