San Francisco Bay

Summary Report on the Transactions of the Smelt Working Group in Water Year 2018

Delta Stewardship Council (Delta Council) | November 1st, 2018

Summary report: Green sturgeon, longfin smelt, and dredging operations in the San Francisco Estuary

San Francisco Estuary Institute (SFEI) | December 1st, 2009

In 2009, California Department of Fish and Game Commission listed longfin smelt (Spirinchus thaleichthys) as threatened, and NOAA formally adopted “take” provisions f

In 2009, California Department of Fish and Game Commission listed longfin smelt (Spirinchus thaleichthys) as threatened, and NOAA formally adopted “take” provisions for green sturgeon (Acipenser medirostris Ayres). These changes in the management status, and associated permitting issues, have prompted renewed interest among [long term management strategy] LTMS participants in the management of these native fish. In response, LTMS held symposia on December 2 and 3, 2009, to review and consider the science, management, and policy related to dredging activities and these species. A primary stressor to both species is reduction of appropriate habitat, due to water diversion activities and other basin-scale modifications in water flow. Local studies of dredging have shown little evidence of direct entrainment for either species, and the frequency of encounter with sites of dredging activity is likely to be very low. Nevertheless, spatial and temporal patterns of population movements and reproductive activity vary from year to year, making it difficult to employ an environmental work windows approach. Available information is limited on other direct effects of dredging, including sediment contamination, habitat modification, and underwater noise. Indirect effects due to maintenance of active navigation channels pose potential concerns. In particular, introduction of invasive species, and mortality due to propeller strikes, both warrant attention. As a follow up step to the symposia, we recommend that LTMS host a workshop targeted towards specific LTMS management needs for green sturgeon and longfin smelt. The workshop should include LTMS participants, the scientists that presented at the symposium, and dredging operators, and could focus on the integration of current research findings into tools that would be useful for managers. Appropriate tools for consideration include predictive or descriptive models of species distribution, and of potential impacts of various dredging activities. There should also be consideration of management approaches that broadly address the primary ecosystem-level stressors for green sturgeon and longfin smelt, rather than employing small scale project-level mitigation. In particular, an integrated regional restoration and monitoring program may be the most effective approach to improve the health of the species.

Support for Sediment Bioaccumulation Evaluation: Toxicity Reference Values for San Francisco Bay

San Francisco Estuary Institute (SFEI) | December 3rd, 2018

This special study of the Regional Monitoring Program for Water Quality in San Francisco Bay was conducted to support the Dredged Material Management Office (DMMO) proces

This special study of the Regional Monitoring Program for Water Quality in San Francisco Bay was conducted to support the Dredged Material Management Office (DMMO) process of evaluating results from bioaccumulation testing performed for routine dredging projects. The goal was to use the current DMMO methodology for selecting Toxicity Reference Values (TRVs) from the US Army Corps of Engineers Environmental Residue-Effects Database (ERED), in order to develop a standard list of TRVs for San Francisco Bay. TRVs are used as a conservative screening tool to efficiently evaluate whether observed invertebrate test organism body burdens could indicate adverse ecological effects on benthic organisms in situ. Currently, there are no published standard TRVs for the Bay, and TRV selection is presently performed on a case-by-case basis during the evaluation of bioaccumulation testing results submitted by individual dredgers. A standard list would promote consistent application of the methodology and improve the efficiency of dredging project evaluations. 

Supporting sustainable groundwater management

California Agriculture (UCANR) | March 13th, 2018

Implementation of the 2014 Sustainable Groundwater Management Act is on schedule. The first phase, completed in 2017, created a new layer of local government —

Implementation of the 2014 Sustainable Groundwater Management Act is on schedule. The first phase, completed in 2017, created a new layer of local government — groundwater sustainability agencies. Now, these new agencies must prepare groundwater sustainability plans. These plans will lay out a basic reckoning for every overdrafted basin: without additional water to replace groundwater pumping or to recharge aquifers, there will be less available to produce food, supply homes and businesses, and ensure there is enough water for the environment.

Suspect Screening and Chemical Profile Analysis of Storm-Water Runoff Following 2017 Wildfires in Northern California

Society of Environmental Toxicology and Chemistry (SETAC) | May 5th, 2022

The combustion of structures and household materials as well as firefighting during wildfires lead to releases of potentially hazardous chemicals directly into the landsc

The combustion of structures and household materials as well as firefighting during wildfires lead to releases of potentially hazardous chemicals directly into the landscape. Subsequent storm-water runoff events can transport wildfire-related contaminants to downstream receiving waters, where they may pose water quality concerns. To evaluate the environmental hazards of northern California fires on the types of contaminants in storm water discharging to San Francisco Bay and the coastal marine environment, we analyzed storm water collected after the northern California wildfires (October 2017) using a nontargeted analytical (NTA) approach. Liquid chromatography quadrupole time-of-flight mass spectrometric analysis was completed on storm-water samples (n = 20) collected from Napa County (impacted by the Atlas and Nuns fires), the city of Santa Rosa, and Sonoma County (Nuns and Tubbs fires) during storm events that occurred in November 2017 and January 2018. The NTA approach enabled us to establish profiles of contaminants based on peak intensities and chemical categories found in the storm-water samples and to prioritize significant chemicals within these profiles possibly attributed to the wildfire. The results demonstrated the presence of a wide range of contaminants in the storm water, including surfactants, per- and polyfluoroalkyl substances, and chemicals from consumer and personal care products. Homologs of polyethylene glycol were found to be the major contributor to the contaminants, followed by other widely used surfactants. Nonylphenol ethoxylates, typically used as surfactants, were detected and were much higher in samples collected after Storm Event 1 relative to Storm Event 2. The present study provides a comprehensive approach for examining wildfire-impacted storm-water contamination of related contaminants, of which we found many with potential ecological risk.

Suspended Sediment Flux in the San Francisco Estuary: Part I—Changes in the Vertical Distribution of Suspended Sediment and Bias in Estuarine Sediment Flux Measurements

Estuaries and Coasts (Springer) | April 22nd, 2020

In this study, we investigate how changes in the vertical distribution of suspended sediment affect continuous suspended sediment flux measurements at a location in the S

In this study, we investigate how changes in the vertical distribution of suspended sediment affect continuous suspended sediment flux measurements at a location in the San Francisco Estuary. Current methods for measuring continuous suspended sediment flux estimates relate continuous estimates of suspended-sediment concentration (SSC) measured at-a-point (SSCpt) to discrete cross-section measurements of depth-averaged, velocity-weighted SSC (SSCxs). Regressions that compute SSCxs from continuous estimates of SSCpt require that the slope between SSCpt and SSCxs, controlled by the vertical distribution of SSC, is fixed. However, in tidal systems with suspended cohesive sediment, factors that control the vertical SSC profile—vertical turbulent mixing and downward settling of suspended sediment mediated by flocculation of cohesive sediment—constantly vary through each tide and may exhibit systematic differences between flood and ebb tides (tidal asymmetries in water velocity or particle size). We account for changes in the vertical SSC profile on estimates of SSCxs using time series of the Rouse number of the Rouse-Vanoni-Ippen equation combined with optical turbidity measurements, a surrogate for SSCpt, to predict SSCxs from 2009 to 2011 and 2013. Time series of the Rouse number were estimated by fitting the Rouse-Vanoni-Ippen equation to SSC estimated from optical-turbidity measurements taken at two elevations in the water column. When accounting for changes in the vertical SSC profile, changes in not only the magnitude but also the direction of cumulative sediment-flux measurements were observed. For example, at a mid-depth sensor, sediment flux estimates changed from − 319 kt (± 65 kt, negative indicating net seaward transport) to 482 kt (± 140 kt, positive indicating net landward transport) for 2009–2011 and from − 388 kt (± 140 kt) to 1869 kt (± 406 kt) for 2013–2016. At the study location, estimation of SSCxs solely from SSCpt resulted in sediment flux values that were underestimates on flood tides and overestimates on ebb tides. This asymmetry is driven by covariance between water velocity and particle settling velocity (Ws) with larger Ws on flood compared to ebb tides. Results of this study indicate that suspended-sediment-flux measurements estimated from point estimates of SSC may be biased if systematic changes in the vertical distribution of SSC are unaccounted for.

Sustainable Groundwater Management Act and Local Agency Formation Commissions

California Association of Local Agency Formation Commissions (CALAFCO) | December 15th, 2016

The purpose of this white paper is to summarize how the Sustainable Groundwater Management Act will impact Local Agency Formation Commissions (LAFCOs) around the State of

The purpose of this white paper is to summarize how the Sustainable Groundwater Management Act will impact Local Agency Formation Commissions (LAFCOs) around the State of California. The paper will use a variety of existing documents and sources to describe SGMA and evaluate how this important new law might affect LAFCOs. It is important to note that LAFCOs do not have a formal role in implementing SGMA; however LAFCO can become involved in a number of ways that will be discussed in this paper. 

Sustainable Landscapes in California: A Guidebook for Commercial and Industrial Site Managers

Pacific Institute | August 20th, 2020

Sustainable landscaping offers a solution in balance with the local climate and ecology, and actively contributes to community and watershed health by providing economic,

Sustainable landscaping offers a solution in balance with the local climate and ecology, and actively contributes to community and watershed health by providing economic, social, and environmental benefits. This guidebook provides simple steps to consider, select, and install sustainable landscaping. Aimed specifically at businesses and communities in California, the guidebook includes information on turf replacement, installation of bioswales and rain gardens, permeable pavement, green roofs, and rain tanks and cisterns. Self-assessments guide the user through the selection and installation process.

Sustainable Water and Environmental Management in the California Bay-Delta

National Academy of Sciences (NAS) | March 29th, 2012

Water management in the California Bay Delta is directed toward providing a more reliable water supply for California, and protecting and rehabilitating the Delta eco

Water management in the California Bay Delta is directed toward providing a more reliable water supply for California, and protecting and rehabilitating the Delta ecosystem, including five endangered and threatened populations and species of fish that live in or migrate through the Delta. However, water management in the Bay and Delta is distributed among many agencies and organizations, a structure that hinders the development and implementation of an integrated, comprehensive plan. As a result, recent Bay Delta planning efforts have not resolved the best plan for the environment or for satisfying anticipated water needs. Challenges include the fact that water scarcity has not been adequately addressed in planning for Delta water and environmental management; the interacting effects of the many environmental stressors that impact the Delta ecosystem, and the many biological and physical effects of climate change. This report discusses the issue of scarcity, factors affecting the listed species and the Delta ecosystem in general, future water-supply and delivery options, scientific uncertainties, the degree of restoration likely to be attainable, and the need for comprehensive planning. Key Messages Planning efforts to implement the two goals of providing a more reliable water supply for California and protecting and rehabilitating the Delta ecosystem have not led to clarity on how the inevitable tradeoffs between the two goals should be managed, particularly when water is in short supply. Climate change is one of most challenging and important issues confronting the management and rehabilitation of the Delta ecosystem. Changes in climate are expected to have profound effects on the physical and ecological structure and functioning of the Delta, as well as on the availability of water in California. Many environmental stressors, including water diversions, contaminants in the water, and introduced species affect the structure and functioning of Delta ecosystems. Interactions among stressors and between stressors and ecosystem processes are widespread and complex. Furthermore, species differ in their responses to stress. This complicates the interpretation and evaluation of the effects of stressors on the ecosystem, and makes it impossible to identify which stressor is the root cause of a certain environmental problem, or even to rank the stressors with any certainty. The large number of stressors, their effects and interactions lead to the conclusion that efforts to eliminate any one stressor are unlikely to reverse declines in listed species. Opportunities exist to mitigate or reverse the effects of many stressors. Continued effects analyses, modeling, and monitoring are necessary to ensure actions taken to rehabilitate the ecosystem are cost-effective. Due to the extensive physical changes that have already taken place and are still occurring in the Delta ecosystem and its tributary watersheds, it will not be possible to restore the habitat to its pre-disturbance state. Delta restoration programs will need to balance consideration of an ecosystem approach with the Endangered Species Act's emphasis on individual species. Assessments suggest that many species will be affected by shifts changes in the pattern and type of precipitation due to climate change. Projected increases in mean sea level and extremes of precipitation have the potential to increase the frequency of levee failures and the inundation of islands, in part because the levees continue to subside due to the oxidation of peat. Sea level rise also has the potential to enhance salt water intrusion and alter water quality. Planning and evaluation of future environmental and economic scenarios will need to address uncertainties in projections, integrated analysis, and the development of risk management strategies. Future planning should also include a climate-change based risk model and analysis that incorporates data on the actual changes in Delta conditions as well as alternative future climate change scenarios and their probability. The instability of levees and the fact that the failure of one levee can affect others are likely to be major issues for achieving any measure of water-supply reliability or ecosystem rehabilitation. Continuing the status quo of improving levees will not always be the most environmentally sustainable or economically defensible response in the years ahead. Science is necessary to inform actions and proposals, but does not provide the entire, prioritized, integrated analysis needed. Societal and political considerations are also important factors in determining the most appropriate policy. Undertaking a comprehensive review of water planning and management functioning would allow California to anticipate future needs such as water scarcity, balanced consideration of all statewide water use practices, and water engineering alternatives. As a result, the Delta would be an effective partner in statewide water management plans. It is likely that the scarcity of water for all needs in the Delta will become severe. While more effective planning is developed, the state will need to use its water resources efficiently and productively. The committee has not analyzed the benefits and disadvantages of an isolated conveyance facility, because not enough specific information was available about it, and therefore there is no recommendation with respect to its adoption as a major part of water management in the Delta. However, the considerations such as the form such a facility would take, its size, location, and the diversion design and operation, including the role of current diversions, should be analyzed as part of any integrated Delta plan, and compared to alternative water management options, including current operations.

Sycamore Alluvial Woodland Habitat Mapping and Regeneration Study

San Francisco Estuary Institute (SFEI) | February 1st, 2017

This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and nat

This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and natural settings. Using an array of ecological and geomorphic field analyses, we discuss site characteristics favorable to SAW health and regeneration, make recommendations for restoration and management, and identify next steps. Findings from this study will contribute to the acquisition, restoration, and improved management of SAW as part of the Santa Clara Valley Habitat Plan (VHP).