Synthesis of data and studies relating to Delta Smelt biology in the San Francisco Estuary, emphasizing water year 2017

Interagency Ecological Program (IEP) | November 1st, 2021

In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious managem

In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious management issue. It is especially contentious with regards to the Delta Smelt (Hypomesus transpacificus), a species endemic to the SFE that has been listed as threatened under the Federal Endangered Species Act and endangered by the State of California. Early studies of Delta Smelt distribution within the SFE suggested that Delta Smelt habitat is determined largely by freshwater flow; however, the exact mechanisms and processes producing such benefits remained unclear. In the summer of 2017, the Flow Alteration Management, Analysis, and Synthesis Team (FLOAT-MAST) was established to analyze, synthesize, and summarize the data collected from the various flow-related monitoring and special studies occurring in 2017(see Table Intro 4). This report will focus on the 2017 summer-fall status of Delta Smelt and its habitat following a record wet year. There has been a long-term decline in the abundance of Delta Smelt associated with a decline in other pelagic fishes. Investigators concluded that the decline has likely been caused by the interactive effects of several causes, including changes in both physical and biotic habitats, many of which are tied to amount and timing of freshwater flow. For this report, we formulated a number of basic predictions about the likely effects of high flows in 2017 on Delta Smelt and their habitat (Table 3). We use a qualitative weight of evidence approach to evaluate whether these predictions were supported by available data. Data sources included a variety of long-term monitoring surveys conducted by Interagency Ecological Program (IEP) agencies, as well as model outputs. Delta Smelt population, health, and life history metrics rarely responded as predicted. Water temperature appears to have a stronger effect on Delta Smelt growth rate and some metrics of life history diversity than outflow or X2 position. Other life history diversity attributes varied but did not appear to be driven by outflow or temperature. Health status was difficult to interpret. Low prevalence of lesions and improved nutritional condition during the drought was contradicted by declining overall population levels. Because of the sparse catches of Delta Smelt in the post-POD years, we consider the data insufficient to reach firm conclusions about the predictions concerning range and distribution of Delta Smelt, especially in the fall. The prediction of high survival was not supported. The 2017 Delta Smelt year class began with poor recruitment in spring of 2017 and below average survival for spring to summer and summer to fall. Thus, low production and low survival led to low abundance of all life stages. During the fall to winter period survival improved, yet the resulting adults were low in number. Foraging success of the fish captured, as measured by stomach fullness, was high for juveniles and adults in 2017 relative to recent years associated with the higher densities of common zooplankton prey that occurred in 2017.

Synthesis of Studies in the Fall Low-Salinity Zone of the San Francisco Estuary, September–December 2011

U.S. Geological Survey (USGS) | July 14th, 2014

In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecolo

In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecological Program to explore hypotheses about the ecological role of low-salinity habitat in the San Francisco Estuary—specifically, hypotheses about the importance of fall low-salinity habitat to the biology of delta smelt Hypomesus transpacificus, a species endemic to the San Francisco Estuary and listed as threatened or endangered under federal and state endangered species legislation. The Interagency Ecological Program is a consortium of 10 agencies that work together to develop a better understanding of the ecology of the Estuary and the effects of the State Water Project and Federal Central Valley Project operations on the physical, chemical, and biological conditions of the San Francisco Estuary. The fall low-salinity habitat investigation constitutes one of the actions stipulated in the Reasonable and Prudent Alternative issued with the 2008 Biological Opinion of the U.S. Fish and Wildlife Service, which called for adaptive management of fall Sacramento-San Joaquin Delta outflow following “wet” and “above normal” water years to alleviate jeopardy to delta smelt and adverse modification of delta smelt critical habitat. The basic hypothesis of the adaptive management of fall low-salinity habitat is that greater outflows move the low-salinity zone (salinity 1–6), an important component of delta smelt habitat, westward and that moving the low-salinity zone westward of its position in the fall of recent years will benefit delta smelt, although the specific mechanisms providing such benefit are uncertain. An adaptive management plan was prepared to guide implementation of the adaptive management of fall low-salinity habitat and to reduce uncertainty. This report has three major objectives: •To provide a summary of the results from the first year of coordinated fall low-salinity habitat studies and monitoring. •To provide a synthesis of the results of the fall low-salinity habitat studies and other ongoing research and monitoring, to determine if the available information supports the hypotheses behind the adaptive management of fall low-salinity habitat as set forth in the adaptive management plan. •To begin to put the results from the fall low-salinity habitat studies into context within the larger body of knowledge regarding the San Francisco Estuary and, in particular, the upper San Francisco Estuary, including the Sacramento-San Joaquin Delta, Suisun Bay, and associated embayments.

System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

California Department of Water Resources (DWR) | August 21st, 2017

Senate Bill (SB) X2 1 mandated and allocated resources for “planning and feasibility studies to identify potential options for the reoperation of the state's flood prot

Senate Bill (SB) X2 1 mandated and allocated resources for “planning and feasibility studies to identify potential options for the reoperation of the state's flood protection and water supply systems that will optimize the use of existing facilities and groundwater storage capacity.” Specifically, SB X2 1 stipulated that the studies shall be designed to determine the potential to achieve integration of flood protection and water supply systems to increase water supply reliability and flood protection, improve water quality, and provide for ecosystem protection and restoration. For this evaluation, a suite of ecosystem evaluation metrics were developed to evaluate the effects of reoperation scenarios simulated in Phases II and III of the SRP. Phase II reoperation scenarios were used to develop and test the ecosystem evaluation framework, and to quantify the effects of reoperation at Shasta and Oroville paired with conjunctive use and spring pulse flows. The next step was studying the ecosystem effects of Forecast-Based-Operation (FBO) at Shasta and Oroville combined with conjunctive use and spring pulse flows. Finally, t additional scenarios were developed and evaluated to explore the sensitivity of ecosystem performance to FBO and the potential for reoperation to enhance major ongoing ecosystem restoration efforts in the system. The purpose of this report is to document and describe the methods and results from the ecosystem evaluation to date, and to outline additional steps that could optimize reoperation scenarios for ecosystem improvement. RELATED DOCUMENTS: System Reoperation Study, Phase 1: Plan of Study System Reoperation Study, Phase 2: Strategy Formulation and Refinement System Reoperation Study, Phase 2: Appendix A: Forecast?Based Operations Analysis System Reoperation Study, Phase 2: Appendix B: Tradeoff Analysis System Reoperation Study, Phase 3 Report: Assessment of Reoperation Strategies System Reoperation, Phase 3: Appendix C: State Water Project and Central Valley Project Integrated Operations Analysis System Reoperation, Phase 3 Appendix D: Ecosystem Evaluation

Systematic Screening of Dams for Environmental Flow Assessment and Implementation

Bioscience (Oxford University Press) | November 30th, 2014

Targeting climate diversity in conservation planning to build resilience to climate change

Ecological Society of America (Wiley) | April 24th, 2015

Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective g

Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective given long-term climate change? Some conservation scientists argue that planning should focus on protecting the abiotic diversity in the landscape, which drives patterns of biological diversity, rather than focusing on the distribution of focal species, which shift in response to climate change. Climate is one important abiotic driver of biodiversity patterns, as different climates host different biological communities and genetic pools. We propose conservation networks that capture the full range of climatic diversity in a region will improve the resilience of biotic communities to climate change compared to networks that do not. In this study we used historical and future hydro-climate projections from the high resolution Basin Characterization Model to explore the utility of directly targeting climatic diversity in planning. Using the spatial planning tool, Marxan, we designed conservation networks to capture the diversity of climate types, at the regional and sub-regional scale, and compared them to networks we designed to capture the diversity of vegetation types. By focusing on the Conservation Lands Network (CLN) of the San Francisco Bay Area as a real- world case study, we compared the potential resilience of networks by examining two factors: the range of climate space captured, and climatic stability to 18 future climates, reflecting different emission scenarios and global climate models. We found that the climate-based network planned at the sub-regional scale captured a greater range of climate space and showed higher climatic stability than the vegetation and regional based-networks. At the same time, differences among network scenarios are small relative to the variance in climate stability across global climate models. Across different projected futures, topographically heterogeneous areas consistently show greater climate stability than homogenous areas. The analysis suggests that utilizing high-resolution climate and hydrological data in conservation planning improves the likely resilience of biodiversity to climate change. We used these analyses to suggest new conservation priorities for the San Francisco Bay Area.

Targeting Public Trust Suits

Social Science Research Network (SSRN) | February 22nd, 2021

The California public trust doctrine empowers private individuals and interest groups to protect the public trust and to enforce state laws that protect the public trust.

The California public trust doctrine empowers private individuals and interest groups to protect the public trust and to enforce state laws that protect the public trust. California has long led the development of the doctrine in the United States, becoming the first state to allow citizen suits to protect the public trust in 1971. A number of other states have followed California’s lead, resulting in a significant expansion in environmental standing. This broadened standing seems to be settled law. In contrast, two California Court of Appeal decisions create some uncertainty about appropriate defendants in public trust lawsuits. These decisions counsel some caution as private parties pick their targets for public trust litigation.

Technical Report for the Interagency Ecological Program (IEP) Pelagic Organism Decline (POD) Workgroup: Assessment of Aquatic Herbicide Use in the Delta

San Francisco Estuary Institute (SFEI) | May 15th, 2006

Since 2001, the California Department of Boating and Waterways (DBW) has conducted an extensive water quality monitoring program in conjunction with its aquatic herbicide

Since 2001, the California Department of Boating and Waterways (DBW) has conducted an extensive water quality monitoring program in conjunction with its aquatic herbicide applications. In this report, the risk quotient calculation method utilized by the Aquatic Pesticide Monitoring Program (a USEPA Tier 1 risk assessment) was used to determine if there are patterns of Level of Concern exceedances that indicate the possibility of adverse impacts on the Delta aquatic ecosystem due to DBW aquatic herbicide applications. Level of Concern exceedances are indicative only of the need for further investigation of an application scenario and do not, in and of themselves, indicate adverse impacts. This type of risk analysis cannot quantify the potential additive or synergistic effects of all pelagic organism stressors (one of which would be aquatic herbicides) within the Delta. This risk assessment indicates that, with the exception of diquat dibromide applications, DBW herbicide applications are unlikely to have the potential to cause Delta ecosystem water quality impacts. While there were a number of Level of Concern exceedances for diquat, DBW and all regulatory agencies involved were aware of this potential prior to application. NOAA Fisheries requested that, when possible, diquat used adjacent to salmon migratory routes should be reduced or avoided when that species is likely to be present. USFWS determined that diquat impact to aquatic invertebrates is minimal, temporary, and not likely to jeopardize Delta smelt but has required avoidance in areas where and when the smelt are known to be present. For 2006, NOAA has allowed DBW to treat sites in April and May with fluridone, which has allowed the use of diquat to be discontinued.

Technical Report on the Scientific Basis for Alternative San Joaquin River Flow and Southern Delta Salinity Objectives

California State Water Resources Control Board (SWRCB) | February 15th, 2012

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wild

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wildlife beneficial uses, water quality objectives for the protection of southern delta agricultural beneficial uses, and the program of implementation for those objectives contained in the 2006 Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (2006 Bay- Delta Plan). Figure 1.1 displays the project area corresponding to SJR flow objectives and program of implementation and Figure 1.2 displays the project area for the southern Delta water quality objectives and program of implementation. The information and analytical tools described in this report (referred to hereafter as Draft Technical Report or Technical Report) are intended to provide the State Water Board with the scientific information and tools needed to consider potential changes to these objectives and their associated program of implementation. In this quasi-legislative process, State Water Board staff will propose amendments to the SJR flow objectives for the protection of fish and wildlife beneficial uses, southern Delta water quality objectives for the protection of agricultural beneficial uses, and the program of implementation contained in the 2006 Bay-Delta Plan. Also, the environmental impacts of these amendments will be evaluated in a Substitute Environmental Document (SED) in compliance with the California Environmental Quality Act. Any changes to water rights consistent with the revised program of implementation will be considered in a subsequent adjudicative proceeding.

Technologies for Passing Fish at Large Dams

California Department of Water Resources (DWR) | June 1st, 2013

Given the possible conditions that may exist in Central Valley streams as the climate warms, many researchers and agencies have recognized the need to evaluate opportunit

Given the possible conditions that may exist in Central Valley streams as the climate warms, many researchers and agencies have recognized the need to evaluate opportunities to provide Central Valley salmonid species access to currently inaccessible habitat (DWR 2008, NMFS 2009, and CA Resources Agency 2009). In addition, Lindley et al. (2007) stated that in order to recover Central Valley salmonids, some populations will need to be established in areas now blocked by dams. “The state should work with dam owners and operators, federal resource management agencies, and other stakeholders to evaluate opportunities to introduce or reintroduce anadromous fish to upper watersheds. Reestablishing anadromous fish, such as salmon, upstream of dams may provide flexibility in providing cold water conditions downstream, and thereby help inform system reoperation.” (CA Resources Agency 2009) The U.S. Bureau of Reclamation dedicates over 1.2 million acre-feet of water, through operation of the Central Valley Project, to fish and wildlife. DWR releases water to meet minimum flow and temperature requirements downstream of Oroville Dam. Climate change may warm rivers and streams, with less water available for ecosystem flow and temperature needs in spring and summer (CA Resources Agency 2009). As temperatures warm, more cold water storage may be needed so that releases can be made to meet temperature requirements downstream. Providing anadromous1 fish passage to areas upstream of reservoirs could eliminate or reduce the need for cold water releases and give water managers additional flexibility in meeting downstream water supply and flood protection needs. In addition, it is prudent to consider fish passage opportunities as part of potential systems reoperations because other agencies are conducting planning efforts for fish passage ...

Testimony of Wade Crowfoot, California Secretary for Natural Resources House Natural Resources Committee Subcommittee on Water, Oceans and Wildlife

Salton Sea Authority | September 24th, 2020

Thank you, Chairman Huffman and members of the Subcommittee for the opportunity to testify today on how the federal government can partner with California to inve

Thank you, Chairman Huffman and members of the Subcommittee for the opportunity to testify today on how the federal government can partner with California to invest resources and efforts to improve and ultimately revitalize conditions at the Salton Sea. I serve as Secretary of the California Natural Resources Agency (CNRA), which is charged with stewarding California’s natural, historical, and cultural resources for current and future generations. As part of that work and under the direction of Governor Gavin Newsom, our Agency is advancing projects at the Salton Sea to tackle pressing environmental issues and improve conditions for the people who live near the Salton Sea. As California’s largest body of water, the Salton Sea has served as a critical wildlife habitat for nearly 100 years, providing a key stopover spot for many special species of resident and migratory birds along the Pacific Flyway. Flows into the Salton Sea have declined in recent years, and the result is a shrinking, increasingly saline lake. As the Sea recedes, previously submerged lakebed is being exposed, reducing habitat and creating dust that can be hazardous as it dries and becomes airborne. These dust emissions present air quality issues that exacerbate public health challenges experienced by local communities in the region, which already has some of the highest childhood asthma rates.