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.

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.

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.

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

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

Sacramento River Temperature Task Group Annual Report of Activities October 1, 2017 through September 30, 2018

Delta Stewardship Council (Delta Council) | November 21st, 2018

Sacramento River Temperature Task Group Annual Report of Activities, October 1, 2015 through September 30, 2016

Delta Stewardship Council (Delta Council) | October 31st, 2016

Safe Drinking Water Plan for California

California State Water Resources Control Board (SWRCB) | June 9th, 2015

In 1993, the California Department of Health Services (CDHS) (now the California Department of Public Health (CDPH) submitted to the Legislature the report entitled, "Dri

In 1993, the California Department of Health Services (CDHS) (now the California Department of Public Health (CDPH) submitted to the Legislature the report entitled, "Drinking Water into the 21st Century: Safe Drinking Water Plan for California" (1993 Plan). In 1996, the California Legislature enacted Senate Bill (SB) 1307 (Chapter 755, Statutes of 1996). SB 1307 amended Health and Safety (H&S) Code Section 116355 to require a periodic update of the original Plan. The issues that were to be addressed were essentially the same as those included in the 1993 Plan. CDPH assembled a team of experts that conducted extensive reviews and analyses, resulting in a draft plan that included an overview of drinking water regulation, reviews and plans for drinking water quality/monitoring and threats, treatment technologies, funding aspects and financial assistance, and a focus on the challenges faced by small drinking water systems. Following the July 1, 2014 transition of the Drinking Water Program to the State Water Board, the draft plan’s recommendations and implementation plan has been enhanced based on the synergies and resources resulting from incorporation of the program into the State Water Board.  California continues to be dependent on a mixture of surface water and groundwater supplies for drinking water. The degree to which each type of supply is used in a given year is dependent upon the region of the state, water needs, water resource availability, and climatologic conditions within the state. During periods of normal to high rainfall, surface water sources make up a higher percentage of the overall drinking water supplies across the state. However, during periods of lower than average rainfall, use of groundwater increases and surface water supplies are strained. As California’s population has grown since the 1993 Plan was published, the demand on the State’s limited water resources have increased. To meet this demand, many public water systems (PWS) have promoted conservation measures as well as looked to other potential sources of supply such as recycled water and desalination. Mirroring the regulatory scope of the Division of Drinking Water, the scope of this Plan focuses on the state’s public water systems (PWS), as defined in Health and Safety Code 116275(h). These are systems that either have (a) 15 or more service connections or (b) systems that serve at least 25 individuals daily at least 60 days out of the year. There are currently more than 7,600 PWS in the state. This is a significant reduction from the more than 10,000 that were in existence in 1993.  However, California’s population has grown from approximately 29 million to over 38 million. Of those 7,600 PWS, approximately seven percent serve communities with more than 10,000 service connections (approximately 33,000 people). The majority of PWS serve smaller communities with more than 63 percent of PWS serving communities with less than 200 service connections (approximately 660 people). Many of the small PWS are challenged by lack of technical, managerial, and financial (TMF) capacity; many do not serve drinking water that meets standards (“safe drinking water”). In 2012, California became the first state to enact a Human Right to Water law, AB 685 (Chapter 524, Statutes of 2012). Public policy continues to be focused on the right of every human being to have safe, clean, affordable, and accessible water adequate for human consumption, cooking, and sanitation. Water supply, contaminants, costs of treatment and distribution systems, the number and nature of small PWSs, especially in disadvantaged communities, and many other factors will continue to challenge progress in addressing the Human Right to Water. The State Water Board is committed to actively pursuing initiatives to address the Human Right to Water, beginning with the state’s residents who are served by PWS but who do not receive safe drinking water.

Safe Drinking Water Plan for California: Report to the Legislature in Compliance with Health and Safety Code Section 116365

California State Water Resources Control Board (SWRCB) | June 8th, 2015

The State Water Board recognizes that to fulfill the Human Right to Water in California, every resident should have access to affordable, safe drinking water regardless

The State Water Board recognizes that to fulfill the Human Right to Water in California, every resident should have access to affordable, safe drinking water regardless of the water system size. Provided data become available on this topic, in a future update of the Safe Drinking Water Plan the Water Board could expand the scope to include systems below 15 service connections, but to do that would require new and expanded authority, significantly more resources, as well as commitment and involvement of other local and state agency partners. At this time, this report contains 32 practical recommendations in 9 areas that would expand the State Water Board’s efforts to bring a greater number of systems into compliance and contribute to realizing the Human Right to Water in California. Each chapter provides a background discussion covering the areas mandated by the Legislature including a description of problems and issues and a set of conclusions and recommendations with the basis and justification for them. A detailed five-year implementation plan addressing the major recommendations is provided in Appendix 10.

Sailing the Salt Line

Bay Nature | July 2nd, 2024

A strait is a place of motion. Change is a constant in our universe, a fact we humans often struggle with, but certain places are especially good at reminding us of it. T

A strait is a place of motion. Change is a constant in our universe, a fact we humans often struggle with, but certain places are especially good at reminding us of it. The Carquinez Strait itself was only just born, some 560,000 years ago—explosively, according to one theory—when a giant inland lake forced a path to the ocean. This created the unusual inverted river delta (with the fan pointing inland, instead of spreading out onto the coast) that is the San Francisco Bay.

Salinity Changes the Dynamics of Pyrethroid Toxicity in Terms of Behavioral Effects on Newly Hatched Delta Smelt Larvae

Toxics (MDPI) | February 20th, 2021

Salinity can interact with organic compounds and modulate their toxicity. Studies have shown that the fraction of pyrethroid insecticides in the aqueous phase increases w

Salinity can interact with organic compounds and modulate their toxicity. Studies have shown that the fraction of pyrethroid insecticides in the aqueous phase increases with increasing salinity, potentially increasing the risk of exposure for aquatic organisms at higher salinities. In the San Francisco Bay Delta (SFBD) estuary, pyrethroid concentrations increase during the rainy season, coinciding with the spawning season of Delta Smelt (Hypomesus transpacificus), an endangered, endemic fish. Furthermore, salinity intrusion in the SFBD is exacerbated by global climate change, which may change the dynamics of pyrethroid toxicity on aquatic animals. Therefore, examining the effect of salinity on the sublethal toxicity of pyrethroids is essential for risk assessments, especially during the early life stages of estuarine fishes. To address this, we investigated behavioral effects of permethrin and bifenthrin at three environmentally relevant concentrations across a salinity gradient (0.5, 2 and 6 PSU) on Delta Smelt yolk-sac larvae. Our results suggest that environmentally relevant concentrations of pyrethroids can perturb Delta Smelt larvae behavior even at the lowest concentrations (<1 ng/L) and that salinity can change the dynamic of pyrethroid toxicity in terms of behavioral effects, especially for bifenthrin, where salinity was positively correlated with anti-thigmotaxis at each concentration.