Physics to Fish: Understanding the Factors that Create and Sustain Native Fish Habitat in the San Francisco Estuary

U.S. Geological Survey (USGS) | January 16th, 2024

The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to impro

The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt (Hypomesus transpacificus) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid (Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California.

Phytoplankton, and Related Water-Quality Constituents in the California Sacramento– San Joaquin Delta at the Landscape Scale: 2018 High Resolution Mapping Surveys

U.S. Geological Survey (USGS) | April 1st, 2024

This study examined the abundance and distribution of nutrients and phytoplankton in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) and Suis

This study examined the abundance and distribution of nutrients and phytoplankton in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) and Suisun Bay, comprising three spatial surveys conducted in May, July, and October of 2018 that used continuous underway high frequency sampling and measurements onboard a high-speed boat to characterize spatial variation across the extent of the Delta. The method used involves simultaneously collecting information about the concentration and spatial distribution of all major nutrient forms with analogous information about the major classes of phytoplankton and associated water-quality conditions. The results showed substantial variation across space and time, providing an unprecedented snapshot of the dynamic environmental processes that shape the ways nutrients interact with and affect aquatic habitats in the Delta.

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: 

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.

Pollutants of concern (POC) loads monitoring progress report, water years (WYs) 2012, 2013, and 2014

San Francisco Estuary Institute (SFEI) | July 1st, 2016

The San Francisco Regional Water Quality Control Board (Water Board) has determined that San Francisco Bay is impaired by mercury and PCBs due to threats to wildlife and

The San Francisco Regional Water Quality Control Board (Water Board) has determined that San Francisco Bay is impaired by mercury and PCBs due to threats to wildlife and human consumers of fish from the Bay. These contaminants persist in the environment and accumulate in aquatic food webs (SFRWRCB 2006; SFRWRCB, 2008). The Water Board has identified urban runoff from local watersheds as a pathway for pollutants of concern into the Bay, including mercury and PCBs. The Municipal Regional Stormwater Permit (MRP; SFRWRCB, 2009) contains several provisions requiring studies to measure local watershed loads of suspended sediment (SS), total organic carbon (TOC), polychlorinated biphenyl (PCB), total mercury (HgT), total methylmercury (MeHgT), nitrate-N (NO3), phosphate-P (PO4), and total phosphorus (TP) (provision C.8.e), as well as other pollutants covered under provision C.14. (e.g. legacy pesticides, PBDEs, and selenium).

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

Preseason Report II Proposed Alternatives and Environmental Assessment Part 2 for 2019 Ocean Salmon Fishery Regulations (PRE II)

Pacific Fishery Management Council | March 21st, 2019

Preseason Report III Council Adopted Management Measures and Environmental Assessment Part 3 for 2019 Ocean Salmon Fishery Regulations (PRE III)

Pacific Fishery Management Council | April 30th, 2019