San Francisco Bay

Fish-Habitat Relationships Along the Estuarine Gradient of the Sacramento-San Joaquin Delta, California: Implications for Habitat Restoration

Estuaries and Coasts (Springer) | June 6th, 2018

Estuaries are highly variable environments where fish are subjected to a diverse suite of habitat features (e.g., water quality gradients, physical structure) that filt

Estuaries are highly variable environments where fish are subjected to a diverse suite of habitat features (e.g., water quality gradients, physical structure) that filter local assemblages from a broader, regional species pool. Tidal, climatological, and oceanographic phenomena drive water quality gradients and, ultimately, expose individuals to other habitat features (e.g., stationary physical or biological elements, such as bathymetry or vegetation). Relationships between fish abundances, water quality gradients, and other habitat features in the Sacramento-San Joaquin Delta were examined as a case example to learn how habitat features serve as filters to structure local assemblages in large river-dominated estuaries. Fish communities were sampled in four tidal lakes along the estuarine gradient during summer-fall 2010 and 2011 and relationships with habitat features explored using ordination and generalized linear mixed models (GLMMs). Based on ordination results, landscape-level gradients in salinity, turbidity, and elevation were associated with distinct fish assemblages among tidal lakes. Native fishes were associated with increased salinity and turbidity, and decreased elevation. Within tidal lakes, GLMM results demonstrated that submersed aquatic vegetation density was the dominant driver of individual fish species densities. Both native and non-native species were associated with submersed aquatic vegetation, although native and non-native fish populations only minimally overlapped. These results help to provide a framework for predicting fish species assemblages in novel or changing habitats as they indicate that species assemblages are driven by a combination of location within the estuarine gradient and site-specific habitat features.

Five Guiding Principles for Effective Voluntary Agreements

University of California, Berkeley (UC Berkeley) | January 3rd, 2024

California has increasingly emphasized efforts to develop voluntary agreements (VAs) with water users as a means of achieving regulatory goals in certain watersheds. In t

California has increasingly emphasized efforts to develop voluntary agreements (VAs) with water users as a means of achieving regulatory goals in certain watersheds. In theory, a VA can combine the protectiveness of a regulatory backstop with the creativity and flexibility of a negotiated deal to produce outcomes as good as, or better than, those achievable through strict application of regulatory requirements alone. However, reality has not always measured up to this ideal. This policy paper uses the Bay-Delta watershed as a case study to inform five principles to guide the appropriate use and evaluation of VAs.

Flame retardants and plastic additives in San Francisco Bay: Targeted monitoring of organophosphate esters and bisphenols

San Francisco Estuary Institute (SFEI) | January 31st, 2020

Flood Risk and Management of California's Sacramento-San Joaquin Delta Levee System

University of California, Santa Cruz (UC Santa Cruz) | September 15th, 2020

Flood Size Increases Nonlinearly Across the Western United States in Response to Lower Snow-Precipitation Ratios

American Geophysical Union (AGU) | December 20th, 2019

Many mountainous and high-latitude regions have experienced more precipitation as rain rather than snow due to warmer winter temperatures. Further decreases in the annual

Many mountainous and high-latitude regions have experienced more precipitation as rain rather than snow due to warmer winter temperatures. Further decreases in the annual snow fraction are projected under continued global warming, with potential impacts on flood risk. Here, we quantify the size of streamflow peaks in response to both seasonal and event-specific rain-fraction using stream gage observations from watersheds across the western United States. Across the study watersheds, the largest rainfall-driven streamflow peaks are >2.5 times the size of the largest snowmelt-driven peaks. Using a panel regression analysis of individual precipitation and snowmelt events, we show that the empirical streamflow response grows approximately exponentially as the liquid precipitation input increases, with rain-dominated runoff leading to proportionately larger streamflow increases than snowmelt or mixed rain-and-snow runoff. We find that the response to changes in rain percentage is largest in the wettest watersheds, where wet antecedent conditions are important for increasing runoff efficiency. Similarly, the effect of rain percentage is larger across watersheds in the Northwest and West regions compared to watersheds in the Northern Rockies and Southwest regions. Overall, as a higher percentage of precipitation falls as rain, increases in the size of rainfall-driven and “rain-on-snow”-driven floods have the potential to more than offset decreases in the size of snowmelt-driven floods.

Flooded Wetland Availability for Breeding Waterfowl in a Mediterranean Climate: Mapping 38 Years of Historical Data in Suisun Marsh, California

University of California, Davis (UC Davis) | December 19th, 2025

Most managed wetlands in California are ephemeral and are purposefully flooded during the fall and winter for over-wintering waterfowl and are dry during the spring and s

Most managed wetlands in California are ephemeral and are purposefully flooded during the fall and winter for over-wintering waterfowl and are dry during the spring and summer waterfowl breeding season. Only semi-permanent and permanent wetlands remain flooded through the critical summer brood-rearing period for ducklings. We examined flooded wetland availability for breeding waterfowl in the brackish Suisun Marsh (California, USA) annually during the spring (April 27–May 17, during peak nesting) and summer (June 17–July 7, during peak duckling brood rearing), for a 38-year period using Landsat satellite imagery and spectral mixture analysis. Flooded wetland area increased 43% in spring and 48% in summer from 1984 to 2021 but varied among years (spring: 37.6–88.6 km2; summer: 17.7–57.5 km2). This increase in flooded wetland area over the past four decades was due to just a few sites, with only 24% (spring) and 15% (summer) of the 198 land-owner parcels increasing in flooded area. Flooded wetland area in the spring was unrelated to annual precipitation between October and April (range: 25–104 cm) or spring precipitation between January and April (range: 8-65 cm), whereas flooded wetland area in the summer was weakly correlated to both annual and spring precipitation. Flooded wetland area in spring and summer was also weakly correlated with the median daily outflow from the Sacramento-San Joaquin River Delta between March 15 and June 15, which corresponds to a critical period of wetland water management for breeding waterfowl. Our results indicate that spring and summer flooded wetland habitat for breeding waterfowl has slightly increased over the past four decades, varies annually, and is mostly dependent on local wetland management practices rather than on precipitation or Delta outflows. Managing habitats as semi-permanent wetlands would increase flooded wetland habitat in the spring and summer and provide habitat for nesting hens and ducklings.

Floods in California

Public Policy Institute of California (PPIC) | February 29th, 2024

Flow Augmentations Modify an Estuarine Prey Field

University of California, Davis (UC Davis) | June 15th, 2023

Flows and Fishes in the Sacramento-San Joaquin Delta

Delta Stewardship Council (Delta Council) | August 1st, 2015

Record-low counts of Delta smelt at a time of persistent drought underscore the importance and challenges of managing freshwater flows for the benefit of fishes in the Sa

Record-low counts of Delta smelt at a time of persistent drought underscore the importance and challenges of managing freshwater flows for the benefit of fishes in the Sacramento-San Joaquin Delta while also meeting human demands for water. Understanding the effects of water flows on fishes is central to understanding how the Delta ecosystem functions and is key to achieving the state’s coequal goals of “providing a more reliable water supply for California and protecting, restoring and enhancing the Delta ecosystem … in a manner that protects and enhances … the values of Delta as an evolving place”. The economic, ecological, and social costs of scientific uncertainty in water management controversies are significant - and to some degree unavoidable. Scientific findings that relate fishes and flows increasingly guide decisions on how to manage flows for the well-being of threatened or endangered species in the Delta. Many studies – and management decisions – rely on correlations between water flows and fish populations. But the decisions warrant fuller understanding of precisely how the flows affect the fishes. Knowledge of these underlying mechanisms is likely to facilitate adaptive management by clarifying uncertainty and risk, by creating specific expectations for outcomes and by strengthening testable hypotheses. This report therefore recommends, first and foremost (there are other recommendations as well), redoubling effects to identify causes and effects concerning fishes and flows in the Delta.

Flows and Fishes in the Sacramento-San Joaquin Delta Research Needs in Support of Adaptive Management

Delta Stewardship Council (Delta Council) | August 15th, 2015