San Francisco Bay

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.

Ridging associated with drought in western and southwestern United States: characteristics, trends and predictability

American Meteorological Society (AMS) | April 1st, 2020

Persistent winter ridging events are a consistent feature of meteorological drought across the western and southwestern United States. In this study, a ridge detection al

Persistent winter ridging events are a consistent feature of meteorological drought across the western and southwestern United States. In this study, a ridge detection algorithm is developed and applied on daily geopotential height anomalies to track and quantify the diversity of individual ridge characteristics (e.g., position, frequency, magnitude, extent, and persistence). Three dominant ridge types are shown to play important, but differing, roles for influencing the location of landfalling atmospheric rivers (ARs), precipitation, and subsequently meteorological drought. For California, a combination of these ridge types is important for influencing precipitation deficits on daily through seasonal time scales, indicating the various pathways by which ridging can induce drought. Furthermore, both the frequency of ridge types and reduced AR activity are necessary features for explaining drought variability on seasonal time scales across the western and southwestern regions. The three ridge types are found to be associated in different ways with various remote drivers and modes of variability, highlighting possible sources of subseasonal-to-seasonal (S2S) predictability. A comparison between ridge types shows that anomalously large and persistent ridging events relate to different Rossby wave trains across the Pacific with different preferential upstream locations of tropical heating. For the “South-ridge” type, centered over the Southwest, a positive trend is found in both the frequency and persistence of these events across recent decades, likely contributing to observed regional drying. These results illustrate the utility of feature tracking for characterizing a wider range of ridging features that collectively influence precipitation deficits and drought.

RipZET: Documentation of Tool Demonstration in Marin County

San Francisco Estuary Institute (SFEI) | March 31st, 2015

The San Francisco Estuary Institute and Aquatic Science Center (SFEI‐ASC) has developed the Riparian Zone Estimation Tool (RipZET) to help the California community of

The San Francisco Estuary Institute and Aquatic Science Center (SFEI‐ASC) has developed the Riparian Zone Estimation Tool (RipZET) to help the California community of riparian interests visualize and characterize riparian areas as habitat unto themselves as well as their capacity to function as buffers for protecting the ecosystem services of the state’s streams, lakes and wetlands. RipZET is a tool used with Geographic Information System (GIS) and spreadsheet software to estimate “functional riparian width,” or the width associated with different riparian functions (e.g., large woody debris input, shading, floodwater storage), which varies with channel type and watershed location. The concept of functional riparian width is central to the riparian definition recommended by the National Research Council (NRC 2002) and is integral in many recently developed riparian design and management guidelines around the country.

Risk-Informed Future Climate Scenario Development for the State Water Project Delivery Capability Report

California Department of Water Resources (DWR) | August 24th, 2023

This report introduces and documents an extensive effort undertaken by the California Department of Water Resources (DWR) to develop risk-informed future climate scenario

This report introduces and documents an extensive effort undertaken by the California Department of Water Resources (DWR) to develop risk-informed future climate scenarios for the State Water Project (SWP) Delivery Capability Report (DCR), a report issued by the SWP every two years. These reports present DWR’s analysis of the SWP system and planning information for users of SWP water. The analysis provides information about how climate change, regulatory, and operational considerations affect SWP delivery capability. Specifically, the report must provide “…under a range of hydrologic conditions, the then existing overall delivery capability of the project facilities and the allocation of that capacity to each contractor. The range of hydrologic conditions shall include the historic extended dry cycle and long-term average.” (Settlement Agreement 2003).

Risks of ocean acidification in the California Current food web and fisheries: ecosystem model projections

Wiley | January 12th, 2017

The benefits and ecosystem services that humans derive from the oceans are threatened by numerous global change stressors, one of which is ocean acidification. Here, we d

The benefits and ecosystem services that humans derive from the oceans are threatened by numerous global change stressors, one of which is ocean acidification. Here, we describe the effects of ocean acidification on an upwelling system that already experiences inherently low pH conditions, the California Current. We used an end‐to‐end ecosystem model (Atlantis), forced by downscaled global climate models and informed by a meta‐analysis of the pH sensitivities of local taxa, to investigate the direct and indirect effects of future pH on biomass and fisheries revenues. Our model projects a 0.2‐unit drop in pH during the summer upwelling season from 2013 to 2063, which results in wide‐ranging magnitudes of effects across guilds and functional groups. The most dramatic direct effects of future pH may be expected on epibenthic invertebrates (crabs, shrimps, benthic grazers, benthic detritivores, bivalves), and strong indirect effects expected on some demersal fish, sharks, and epibenthic invertebrates (Dungeness crab) because they consume species known to be sensitive to changing pH. The model's pelagic community, including marine mammals and seabirds, was much less influenced by future pH. Some functional groups were less affected to changing pH in the model than might be expected from experimental studies in the empirical literature due to high population productivity (e.g., copepods, pteropods). Model results suggest strong effects of reduced pH on nearshore state‐managed invertebrate fisheries, but modest effects on the groundfish fishery because individual groundfish species exhibited diverse responses to changing pH. Our results provide a set of projections that generally support and build upon previous findings and set the stage for hypotheses to guide future modeling and experimental analysis on the effects of OA on marine ecosystems and fisheries.

River Floods Under Wetter Antecedent Conditions Deliver Coarser Sediment to the Coast

American Geophysical Union (AGU) | April 13th, 2025

Increasing hydrologic volatility—more extreme rain, and larger variations between wet and dry years—has become apparent in some regions, but few data exist to determi

Increasing hydrologic volatility—more extreme rain, and larger variations between wet and dry years—has become apparent in some regions, but few data exist to determine how intensifying hydrologic extremes affect sedimentary systems. Using uniquely high-resolution records of fluvial suspended sediment and coastal morphology, we quantify sedimentary responses from a steep, 357-km2 watershed in California under extreme wet and dry hydrologic conditions. In years with multiple 2- to 10-year floods, fluvial sediment coarsened significantly as the wet season progressed, with late-season floods delivering dominantly sand-sized material to the coast. Greater and coarser sediment supply under wetter antecedent conditions affected nearshore geomorphic evolution for 4–5 years. The watershed and coastal changes we documented point to an increasing role of sediment-related hazards (flooding and hillslope erosion) and resources (nearshore accretion) as wet seasons intensify.

Rivers of California

Pacific Gas & Electric Company (PG&E) | July 1st, 1962

Ruling on Motions for Preliminary Injunction in Tulare Lake Basin Water Storage District v. California Department of Water Resources

Superior Court of California, County of Sacramento | June 20th, 2024

Sacramento and San Joaquin River Basins Comprehensive Study Technical Studies Documentation: Reservoir Operations Modeling - Existing Design Operations and Re-operation Analyses

U.S. Army Corps of Engineers (USACE) | December 1st, 2002

In response to extensive flooding and damages experienced in 1997, the United States Congress authorized the U.S. Army Corps of Engineers, Sacramento District (USACE) to

In response to extensive flooding and damages experienced in 1997, the United States Congress authorized the U.S. Army Corps of Engineers, Sacramento District (USACE) to provide a comprehensive analysis of the Sacramento and San Joaquin river basin flood management systems and to partner with the State of California to develop master plans for flood damage reduction. The USACE and the State Reclamation Board of California are leading this Comprehensive Study to improve flood management and integrate ecosystem restoration in the Sacramento and San Joaquin river basins. The authorization for the Comprehensive Study directed the development of hydrologic and hydraulic models for both river basins that will allow systematic evaluation. These models incorporate reservoir operations and flow along the major river systems to evaluate the performance of the flood management systems. The models can be used to assess the performance of the current systems or modified systems under a wide range of hydrologic conditions. This report documents the work conducted for the Sacramento and San Joaquin River Basins Comprehensive Study to develop reservoir operation models, specifically Phase II – Model Refinement and Simulation of both existing operational conditions and evaluation of flood management alternatives. The main product components of this effort include: HEC-5 Reservoir Operation Models for the Sacramento and San Joaquin River basins, which will include headwater and major flood management reservoirs. The first part of this document is limited to the use of reservoir models to identify and describe baseline conditions. It does not include the formulation or evaluation of flood management alternatives. The performance of modified flood management strategies is addressed within subsequent sections of this document. Future work will continue to use these models in the analysis of alternatives for reducing flood damages in California’s Central Valley.

Sacramento River Temperature Task Group Annual Report of Activities October 1, 2013 through September 30, 2014

Delta Stewardship Council (Delta Council) | October 6th, 2014