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.

Technical Approach to Develop Nutrient Numeric Endpoints for California

California State Water Resources Control Board (SWRCB) | July 31st, 2006

This report provides an approach for the development of nutrient (nitrogen and phosphorus) numeric endpoints for use in the water quality programs of the California’s S

This report provides an approach for the development of nutrient (nitrogen and phosphorus) numeric endpoints for use in the water quality programs of the California’s State Water Resources Control Board (State Water Board) and Regional Water Quality Control Boards (Regional Water Boards). The approach provides a methodology to support several water quality program components including: setting numeric limits for National Pollutant Discharge Elimination System (NPDES) permits; development of Total Maximum Daily Load (TMDL) nutrient numeric endpoints; and for those Regional Water Boards that choose to, the development of numeric nutrient criteria. Guidance for this technical report comes from participants at workshop (Nutrient Numeric Endpoints Training Workshop held on May 18 & 19 2005 in Sacramento, CA) that is a part of a longer running process that has been sponsored by EPA Region IX and the State Water Board.   The workshop summary (Summary of May 18-19, 2005 Nutrient Workshop) of this workshop can be downloaded from the project website: http://rd.tetratech.com/epa/. The CA Nutrient Numeric Endpoints process includes a Regional Technical Advisory Group (RTAG); and a collaborative forum of Regional Water Boards, Tribes, and other state and federal agencies in the State Regional Technical Advisory Group (STRTAG). The result of the RTAG / STRTAG process is an approach that has achieved a high level of consensus among participants. The purpose of this document is to describe the approach that has been reviewed and approved by the STRTAG. The intention of the proposed approach is to select nutrient response indicators that can be used to evaluate risk of use impairment, rather than using pre-defined nutrient limits that may or may not result in eutrophication for a particular water body. The report provides a description of the proposed approach that includes innovative elements such as: A water body classification framework that uses three Beneficial Use risk classification categories; Risk-based secondary indicators that are more closely linked to Beneficial Use condition than water column nutrient concentrations; and Modeling tools that provide the necessary linkage analysis between secondary indicators and water column nutrient concentrations. The modeling tools also account for site-specific cofactors such as flow, light availability, and others. This report provides the starting point for a process that will lead to refinements in the classification framework, secondary indicators, and linkage analysis modeling tools through the development of site-specific endpoints. The report has been reviewed by workshop participants; other State, Federal, and Tribal staff; and the Technical Evaluation Committee identified in Appendix 1. This report includes changes made in response to comments received. As an adaptive management process technical updates will be made and new dated editions of this document will be made available. A potential outcome of this process is the adoption of the framework and endpoints by various Regional Water Quality Control Boards for use as nutrient numeric criteria.

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.

The Economic Value of Nature's Services and its role in Integrated Water Management: Four California Case Studies

California Department of Water Resources (DWR) | July 1st, 2014

Here we present four case studies of integrated regional water management that include enhancement of biological diversity among their goals. Each pilot-scale project foc

Here we present four case studies of integrated regional water management that include enhancement of biological diversity among their goals. Each pilot-scale project focuses on multiple water-related natural resources in a defined geographic area, usually a watershed. A common element of the projects is to show the economic benefits of protecting and restoring natural resources in a manner that allows their continued use over the long term. One of the aims of the projects is to recognize the economic value of the goods and services that nature provides and to incorporate that value into natural resource management decisions. Such recognition includes development of ways to measure the economic value of those services. This can be important information for water managers who normally see only the costs of ecosystem protection and restoration, but not the benefits, in their budgets. The goods and services considered in these projects include water supply, water quality, erosion prevention, wildfire prevention, hydropower generation, wood products, flood attenuation, carbon sequestration, land subsidence reversal, and fish and wildlife. Collectively, the projects constitute on-the-ground efforts to advance several of the objectives in the implementation plan of Water Plan 2009. In particular, they aim to expand integrated regional water management (objective 1), protect surface water and groundwater quality (objective 4), expand environmental stewardship (objective 5), practice integrated flood management (objective 6) and manage a sustainable California Delta (objective 7). The case studies accomplish and document several key ingredients of integrated resource management--although no single study does all of them. They identify and involve watershed stakeholders, both managers and users of natural resources. In turn, the stakeholders come to agreement about how they want the watershed to look or function, usually in terms of the goods and services that they want the watershed to provide. Then they reach agreement on a set of management practices that can support and enhance those services and move the watershed toward the desired condition. Finally, the case studies seek to estimate the amounts of goods and services derived from specific management practices. The pilot projects go beyond most watershed management efforts and most ecosystem services work in laying the foundation for establishment of markets for nature’s services, that is, mechanisms for beneficiaries to pay producers for goods and services they receive. This requires some sort of assessment of the monetary value of the benefits. One desired end product is to put payments in the hands of producers-- that is, resource managers—as an incentive to keep them producing.

The San Francisco Bay-Delta Agreement: Principles for Agreement on Bay-Delta Standards Between the State of California and the Federal Government

California State Water Resources Control Board (SWRCB) | December 15th, 1994

The Status of Rainbow Trout (Oncorhynchus mykiss) in the Stanislaus River Summary report of 2015 snorkel surveys

Delta Stewardship Council (Delta Council) | August 1st, 2016

The Vernalis Adaptive Management Program (VAMP): Report of the 2010 Review Panel

California State Water Resources Control Board (SWRCB) | May 11th, 2010

Panel members were asked by the Delta Science Program to carry out an independent review of a 12-year VAMP (Vernalis Adaptive Management Plan) experimental program design

Panel members were asked by the Delta Science Program to carry out an independent review of a 12-year VAMP (Vernalis Adaptive Management Plan) experimental program designed to develop water management measures that would provide protection to juvenile Chinook salmon migrating through the San Joaquin River system and associated Sacramento-San Joaquin River Delta (Delta) waterways. The Charge to the Panel was expressed as a series of three questions that the Panel was obligated to address: 1) Do the results to date from the VAMP study provide useful scientific information about the relationship between salmon survival and each of the following factors: Flows, Exports, and Barrier installation at the head of Old River? 2) How can the results from the VAMP to date be used to inform the State Water Resources Control Board's (SWRCB) current efforts to review and potentially revise the San Joaquin River flow objectives and their implementation? 3) How can the experiences to date from the VAMP study be used in a scientific manner to inform future monitoring and study efforts related to determining appropriate flow, operational, and water quality requirements to protect San Joaquin River fisheries (specifically Chinook salmon and steelhead)?

Thermal performance in juvenile hatchery Oncorhynchus tshawytscha: aerobic scope tests over a range of environmental temperatures

U.S. Environmental Protection Agency (EPA) | March 15th, 2016

In heavily-altered ecosystems, anthropogenic factors coupled with global climate change have drastically changed available habitats for many native fishes (Cloe

In heavily-altered ecosystems, anthropogenic factors coupled with global climate change have drastically changed available habitats for many native fishes (Cloern and Jassby 2012, Moyle et al. 2013). Water projects such as large hydropower dams have altered flow and temperature regimes (Poff et al. 1997, Bunn and Arthington 2002, Marchetti and Moyle 2001), and reduced or degraded native spawning and rearing habitats (Sheer and Steel 2006, Pelicice and Agostinho 2008), while global climate change has resulted in warmer overall river temperatures (Cloern and Jassby, 2012). As ecologically relevant environmental variables like temperature have shifted, fish populations have subsequently declined (Cloern and Jassby, 2012; Hanak et al., 2015). Native California fishes have been disproportionately affected by these changes, and precipitous population declines have been observed for several species, some of which are listed under the Endangered Species Act (ESA) (Moyle et al. 2013). Despite documented correlations between fish declines and changes in environmental variables such as temperatur e (Moyle and Leidy, 1992; Moyle et al. 2010; Quiñones and Moyle 2014), there has been a profound lack of data available on the actual physiological and/or behavioral mechanisms driving fish population declines. Physiological performance data, such as information on aerobic scope, may help provide mechanistic explanations for both how and why fish population declines are occurring. Furthermore, as populations decline and management becomes more crucial for population persistence, thermal limits, optimal thermal ranges, and data on how key physiological processes, such as metabolic rate, change in response to environmental variables becomes more important. Therefore, the objectives of our study were to quantify the aerobic scope of juvenile Chinook salmon ( Oncorhynchus tshawytscha) acclimated to two different rearing temperatures (14 or 20 °C) and tested over a temperature range of 12-26°C.

Toward climate-resilient fisheries in the Humboldt Current: Developing a scientific foundation for improved adaptive management

Environmental Defense Fund (EDF) | January 2nd, 2020

The HCS covers an area comprised of 55° of latitude off Peru and Chile (3°23.57′ to 58°21.02′) and extends over 200 nautical miles offshore. The dynamics of the HC

The HCS covers an area comprised of 55° of latitude off Peru and Chile (3°23.57′ to 58°21.02′) and extends over 200 nautical miles offshore. The dynamics of the HCS are strongly influenced by seasonal or permanent coastal upwelling. Several features distinguish the HCS from similar ecosystems associated with the Eastern Boundary Upwelling Systems of the world’s oceans (EBUS: California, Canarias, Humboldt and Benguela). First, it extends closest to the equator. Second, it is the most exposed EBUS system to ENSO, the largest source of interannual climatic variability on the planet. Third, although each of the EBUS has similar levels of primary productivity, the HCS contains the most productive fisheries. Lastly, it is associated with the presence of a shallow, intense subsurface oxygen minimum layer that compresses the oxygenated epipelagic habitat to a few dozen meters. Global warming is altering energy and matter exchange between the atmospheric, oceanic, and continental boundaries.