Restoring the Heart of a Healthy Estuary: A Review of Restoration in the Sacramento–San Joaquin Delta and Suisun Marsh

Publisher not available | December 19th, 2025

The restoration of native species-dominated ecosystems is critical for improving ecosystem health and meeting policy goals in the Sacramento–San Joaquin Delta and Suisu

The restoration of native species-dominated ecosystems is critical for improving ecosystem health and meeting policy goals in the Sacramento–San Joaquin Delta and Suisun Marsh (upper San Francisco Estuary, collectively), one of the largest estuarine systems in North America. To accomplish large-scale restoration in this heavily altered system, a variety of projects, programs, and motivations inform restoration planning and implementation. Chapter 4 of the Delta Plan synthesizes restoration goals across these efforts to produce comprehensive ecosystem restoration targets of between 60,000 and 80,000 acres across seven ecosystem types by 2050, but a comprehensive review of restoration progress and planning to date is needed. To fill this gap, this paper analyzes the current state of ecosystem restoration in the upper San Francisco Estuary in the context of the Delta Plan targets. We review current scientific and management literature and implementation approaches, and synthesize acreage totals across completed, in-progress, and planned projects for four ecosystem types where substantial development of restoration in the system has occurred: tidal wetland, non-tidal wetland, riparian, and floodplain. We find that tidal wetland restoration has progressed more rapidly than other ecosystem types, motivated by mitigation requirements related to the federal Endangered Species Act. Across all ecosystem types, we identify both promising progress and clear needs for accelerated planning and implementation of restoration projects to meet Delta Plan 2050 targets, and discuss ongoing needs related to science, funding, and implementation.

Retiring Poisoned Lands in the Western San Joaquin Valley: A C-WIN Policy Brief

California Water Impact Network (C-WIN) | January 1st, 2012

It is the policy of the California Water Impact Network to: •Retire poisoned lands from irrigation so that pollution from naturally high levels of contaminants such

It is the policy of the California Water Impact Network to: •Retire poisoned lands from irrigation so that pollution from naturally high levels of contaminants such as salt, selenium, boron, mercury, arsenic and molybdenum is ended. •End wasteful and unreasonable uses of water as mandated under the California Constitution. •Slow or stop the spread of contamination to drinking water supplies, aquifers and aquatic food webs (including those with anadromous fish) where it now occurs, thereby protecting human and public health. •Redirect as much as 4 million acre-­feet of fresh water freed from retired lands to other beneficial uses within the Central Valley watershed, including fish and wildlife refuges, Delta ecosystem restoration and instream flows, and drought-­period municipal uses. •Require that solutions for retiring the poisoned lands from irrigation result in either no net change or an actual net decrease in energy consumption associated with use of those lands.

Review of and recommendations for monitoring contaminants and their effects in the San Francisco Bay−Delta

University of California, Davis (UC Davis) | December 3rd, 2019

Legacy and current-use contaminants enter into and accumulate throughout the San Francisco Bay−Delta (Bay−Delta), and are present at concentrations with known effects

Legacy and current-use contaminants enter into and accumulate throughout the San Francisco Bay−Delta (Bay−Delta), and are present at concentrations with known effects on species important to this diverse watershed. There remains major uncertainty and a lack of focused research able to address and provide understanding of effects across multiple biological scales, despite previous and ongoing emphasis on the need for it. These needs are challenging specifically because of the established regulatory programs that often monitor on a chemical-by-chemical basis, or in which decisions are grounded in lethality-based endpoints. To best address issues of contaminants in the Bay−Delta, monitoring efforts should consider effects of environmentally relevant mixtures and sub-lethal impacts that can affect ecosystem health. These efforts need to consider the complex environment in the Bay−Delta, including variable abiotic (e.g., temperature, salinity) and biotic (e.g., pathogens) factors. This calls for controlled and focused research, and the development of a multi-disciplinary contaminant monitoring and assessment program that provides information across biological scales. Information gained in this manner will contribute toward evaluating parameters that could alleviate ecologically detrimental outcomes. This review is a result of a Special Symposium convened at the University of California−Davis (UCD) on January 31, 2017 to address critical information needed on how contaminants affect the Bay−Delta. The UCD Symposium focused on new tools and approaches for assessing multiple stressor effects to freshwater and estuarine systems. Our approach is similar to the recently proposed framework laid out by the U.S. Environmental Protection Agency (USEPA) that uses weight of evidence to scale toxicological responses to chemical contaminants in a laboratory, and to guide the conservation of priority species and habitats. As such, we also aimed to recommend multiple endpoints that could be used to promote a multi-disciplinary understanding of contaminant risks in Bay−Delta while supporting management needs.

Review of SWRCB’s “Working Draft Scientific Basis Report for New and Revised Flow Requirements on the Sacramento River and Tributaries, Eastside Tributaries to the Delta, Delta Outflow, and Interior Delta Operations”

Delta Stewardship Council (Delta Council) | February 23rd, 2017

Insightful, informative, well-illustrated, clearly written—these are among our overall impressions of “Working Draft Scientific Basis Report for New and Revised Flow

Insightful, informative, well-illustrated, clearly written—these are among our overall impressions of “Working Draft Scientific Basis Report for New and Revised Flow Requirements on the Sacramento River and Tributaries, Eastside Tributaries to the Delta, Delta Outflow, and Interior Delta Operations”. The comments below focus on recommended improvements. In particular, we recommend clarifying, and further justifying scientifically, the proposed use of percent of “unimpaired flow” as the main basis for establishing an annual environmental water budget. We also suggest presenting a further review of cold-water management, a deeper analysis of non-flow stressors, additional consideration of near-term responses to climate change, and elaboration of how regulations managed adaptively may improve scientific understanding of environmental flows.

Review of the Long-Term Operations of the Central Valley Project and the State Water Project

National Academy of Sciences (NAS) | November 10th, 2025

The CVP and SWP (referred to collectively as “the Projects”) rarely deliver their full contracted  amount of water. Some of this is inherent in the operation of larg

The CVP and SWP (referred to collectively as “the Projects”) rarely deliver their full contracted  amount of water. Some of this is inherent in the operation of large water projects with diverse demands in a dry and highly variable climate. A growing, complex regulatory environment of state and federal laws, some of which were created to protect fish species endemic to the Delta, has further restricted CVP and SWP operations.  These fish include the southern distinct population segment of North American green sturgeon, California Central Valley steelhead, Central Valley spring-run Chinook salmon, Sacramento River winter-run Chinook salmon, longfin smelt, and Delta smelt. Operating the Projects while trying to prevent species extinction can be a source of conflict if the actions to prevent extinction reduce the amount of water that can be exported. Project operation into the future will likely become more challenging as changes in various climatic factors push the listed species closer to their thresholds of survivability. Hence, in late 2023 USBR contracted with the National Academies of Sciences, Engineering, and Medicine (NASEM) to form an expert committee that could serve as an independent review for the CVP and SWP as they operate into the future. The Committee’s statement of task appears in Box S-1. The three actions chosen for the study—the Shasta Coldwater Pool Management Action, the Old and Middle River Flow Management Action, and the Summer-Fall Habitat Action for Delta Smelt— are perceived as consequential for species survival and controversial for their effects on water deliveries to contractors.

Review of the Monitoring Enterprise in the Sacramento-San Joaquin Delta

Delta Stewardship Council (Delta Council) | March 3rd, 2022

Review of the Monitoring Enterprise in the Sacramento-San Joaquin Delta Summary Sheet

Delta Stewardship Council (Delta Council) | April 28th, 2022

Revised Incidental Take Methodology for the Coordinated Long-Term Operation of the CVP and SWP

U.S. Fish and Wildlife Service (FWS) | January 30th, 2019

Revised Water Right Decision 1641

California State Water Resources Control Board (SWRCB) | December 29th, 1999

Revisiting chlorophyll a thresholds for San Francisco Bay: Insights from observations of phytoplankton molecular abundance

Elsevier | February 14th, 2026

Harmful Algal Blooms (HABs) are a hazard for coastal environments worldwide; identifying screening thresholds of chlorophyll-a (chl-a) associated with inc

Harmful Algal Blooms (HABs) are a hazard for coastal environments worldwide; identifying screening thresholds of chlorophyll-a (chl-a) associated with increased risk of HABs is a management priority. Molecular surveillance of coastal phytoplankton and bivalve biotoxins could be used to link chl-a with HAB risk, but requires an understanding of whether the HAB risks increase uniformly as chl-a rises, or whether some taxa are disproportionately favored, and if these relationships vary by season. In this study, we present a novel use of molecular abundance data to investigate the scientific bases for estuarine chl-a thresholds protective against HABs. In San Francisco Bay (SFB), California, the relationship between molecular relative abundance (as measured by 18S metabarcoding) of nine different HAB taxa, absolute quantitative polymerase chain reaction (qPCR) abundance, and mussel toxin concentrations of a subset of the taxa were investigated for thresholds as a function of increasing chl-a. Our results show most HAB taxa did not increase in absolute or relative abundance during SFB’s spring bloom interval, when chl-a levels were highest (>10 µg/L) but the assemblage was dominated by non-harmful diatoms. However, several flagellated, mixotrophic taxa did increase above their molecular baseline in fall, and the combined probability of any HAB occurring above baseline was elevated when chl-a reached ∼4.6 µg/L in the fall. This work demonstrates the promise of molecular approaches in disentangling the seasonally complex interplay between stressors and phytoplankton/HAB community responses and has the potential to provide clearer, more cost-effective monitoring and mitigation strategies for managers.