Fish Restoration Program Agreement Implementation Strategy for Habitat Restoration and Other Actions for Listed Delta Fish

California Department of Water Resources (DWR) | March 6th, 2012

The Fish Restoration Program Agreement (FRPA) (Appendix A), between the Department of Fish and Game (DFG) and the Department of Water Resources (DWR), was signed on Octob

The Fish Restoration Program Agreement (FRPA) (Appendix A), between the Department of Fish and Game (DFG) and the Department of Water Resources (DWR), was signed on October 18, 2010. FRPA addresses specific habitat restoration requirements of the US Fish and Wildlife Service (USFWS) and National Marine Fisheries Service (NMFS) biological opinions (Biological Opinions) for State Water Project (SWP) and Central Valley Project (CVP) operations. FRPA is also intended to address the habitat requirements of the DFG Longfin Smelt Incidental Take Permit (ITP) for SWP Delta operations. The primary objective of the FRPA program is to implement the fish habitat restoration requirements and related actions of the Biological Opinions and the ITP in the Delta, Suisun Marsh, and Yolo Bypass and is focused on 8,000 acres of intertidal and associated subtidal habitat to benefit delta smelt, including 800 acres of mesohaline habitat to benefit longfin smelt, and a number of related actions for salmonids. DFG and DWR intend that habitat restoration actions implemented in compliance with the USFWS biological opinion that also meet the habitat restoration requirements of the ITP will operate to satisfy the acreage requirements of the ITP. The purpose of this Implementation Strategy is to describe the process by which DWR and DFG will implement the FRPA program, and to satisfy Section B of FRPA. Section B of FRPA requires DWR, with assistance from DFG, to develop an Implementation Schedule that will identify restoration actions, estimated costs, targeted acreage, and a timeline for DWR’s implementation of restoration actions to satisfy DWR’s obligations under the Biological Opinions and ITP. Appendix B lists the specific habitat restoration requirements of FRPA, the Biological Opinions, and the ITP that pertain to this program. This document lays out the strategy to address these requirements. In addition, DWR and DFG will complete the necessary environmental compliance documents to implement site specific habitat restoration projects; this may include tiering from existing programmatic documents where appropriate. Pursuant to FRPA, DFG will work cooperatively with and assist DWR in establishing the management and financial framework necessary to implement the FRPA program. DWR, with assistance from DFG, will begin a process to fund, plan, and implement actions, including aquatic habitat restoration to benefit delta smelt, longfin smelt, and winter-run and spring-run Chinook salmon (hereafter referred to as Covered Fish Species) to mitigate impacts to these species caused by the SWP Delta operations. Specifically, these actions include: • Delta Smelt Biological Opinion Reasonable and Prudent Alternative (RPA) Component 4; • NMFS Biological Opinion RPA Actions 1.2.6 and 1.6.2 in partnership with the US Bureau of Reclamation (Reclamation); • NMFS Biological Opinion RPA Action Suite 1.6 and 1.7. FRPA will not be lead, but will provide funding and technical support assistance only; • ITP Condition 7. DWR’s obligations focus on delta smelt, longfin smelt, and winter-run and spring-run salmon, and may also benefit steelhead, sturgeon, and other native fish species.

Fish-Habitat Relationships Along the Estuarine Gradient of the Sacramento-San Joaquin Delta, California: Implications for Habitat Restoration

Estuaries and Coasts (Springer) | June 6th, 2018

Estuaries are highly variable environments where fish are subjected to a diverse suite of habitat features (e.g., water quality gradients, physical structure) that filt

Estuaries are highly variable environments where fish are subjected to a diverse suite of habitat features (e.g., water quality gradients, physical structure) that filter local assemblages from a broader, regional species pool. Tidal, climatological, and oceanographic phenomena drive water quality gradients and, ultimately, expose individuals to other habitat features (e.g., stationary physical or biological elements, such as bathymetry or vegetation). Relationships between fish abundances, water quality gradients, and other habitat features in the Sacramento-San Joaquin Delta were examined as a case example to learn how habitat features serve as filters to structure local assemblages in large river-dominated estuaries. Fish communities were sampled in four tidal lakes along the estuarine gradient during summer-fall 2010 and 2011 and relationships with habitat features explored using ordination and generalized linear mixed models (GLMMs). Based on ordination results, landscape-level gradients in salinity, turbidity, and elevation were associated with distinct fish assemblages among tidal lakes. Native fishes were associated with increased salinity and turbidity, and decreased elevation. Within tidal lakes, GLMM results demonstrated that submersed aquatic vegetation density was the dominant driver of individual fish species densities. Both native and non-native species were associated with submersed aquatic vegetation, although native and non-native fish populations only minimally overlapped. These results help to provide a framework for predicting fish species assemblages in novel or changing habitats as they indicate that species assemblages are driven by a combination of location within the estuarine gradient and site-specific habitat features.

FLOOD- MAR Using Flood Water for Managed Aquifer Recharge to Support Sustainable Water Resources

California Department of Water Resources (DWR) | June 26th, 2018

The effects of climate change are necessitating wholesale changes in how water is managed in California.  With less water storage from snowpack, California needs to leve

The effects of climate change are necessitating wholesale changes in how water is managed in California.  With less water storage from snowpack, California needs to leverage both the current water system and new opportunities to provide sustainable alternatives that can simultaneously accommodate longer and deeper droughts, and more severe, and frequent, episodic and seasonal flooding. This recent cycle of drought and flood, and the passage of the Sustainable Groundwater Management Act (SGMA), provide an enhanced opportunity to modernize State policies related to the nexus between flood management, land use, groundwater management, and ecosystem enhancement. Partnerships, among DWR; other State, federal, tribal, regional, and local entities; and university and private researchers, are actively exploring opportunities to determine how flood and groundwater management can be integrated for multiple benefits. Although integrating flood and groundwater management is not a new concept, the time is ripe to implement an expanded, large-scale integrated program. With the passage and early implementation of SGMA, in combination with climate-induced extreme events, the logic for communities to partner and integrate is evident and imperative. This partnership will help reduce the impacts of future swings between high- and low-flow periods while meeting their communities’ objectives, with the added benefits of improving floodplain ecosystems, preserving working landscapes, and engaging California’s agricultural community in needed solutions, among others. This white paper explores “Flood-MAR”, an integrated and voluntary resource management strategy that uses flood water resulting from, or in anticipation of, rainfall or snowmelt for groundwater recharge on agricultural lands and working landscapes, including but not limited to refuges, floodplains, and flood bypasses. Large-scale implementation of Flood-MAR will fundamentally change how flood and groundwater management are managed. Flood-MAR can be implemented at multiple scales, from individual landowners diverting flood water with existing infrastructure, to using extensive detention/recharge areas and modernizing flood protection infrastructure/operations. Flood-MAR’s potential and value for California is achieved by integrating Flood-MAR with other regional recharge efforts, changing management of California’s water system to better integrate surface water and groundwater, upgrading conveyance, storage, and operations, and considering Flood-MAR’s opportunities as related to water transport and transfers are some of the system integration considerations. This white paper demonstrates the need for Flood-MAR to become an important part of California’s portfolio of water resource management strategies, now and in the future, to help significantly improve water resources sustainability and climate resiliency throughout the state.  Using Flood Water for Managed Aquifer Recharge Can Provide Broad Benefits. There is a clear State interest in encouraging, and participating in, Flood-MAR projects because they can provide broad and multiple public and private benefits for Californians and the ecosystems of the state. Potential public benefits include: - Flood Risk Reduction. - Drought Preparedness. - Aquifer Replenishment. - Ecosystem Enhancement. - Subsidence Mitigation. - Water Quality Improvement. - Working Landscape Preservation and Stewardship.

Floodplain farm fields provide novel rearing habitat for Chinook salmon

PLOS | June 7th, 2016

When inundated by floodwaters, river floodplains provide critical habitat for many species of fish and wildlife, but many river valleys have been extensively leveed and f

When inundated by floodwaters, river floodplains provide critical habitat for many species of fish and wildlife, but many river valleys have been extensively leveed and floodplain wetlands drained for flood control and agriculture. In the Central Valley of California, USA, where less than 5% of floodplain wetland habitats remain, a critical conservation question is how can farmland occupying the historical floodplains be better managed to improve benefits for native fish and wildlife. In this study fields on the Sacramento River floodplain were intentionally flooded after the autumn rice harvest to determine if they could provide shallow-water rearing habitat for Sacramento River fall-run Chinook salmon (Oncorhynchus tshawytscha). Approximately 10,000 juvenile fish (ca. 48 mm, 1.1 g) were reared on two hectares for six weeks (Feb-March) between the fall harvest and spring planting. A subsample of the fish were uniquely tagged to allow tracking of individual growth rates (average 0.76 mm/day) which were among the highest recorded in fresh water in California. Zooplankton sampled from the water column of the fields were compared to fish stomach contents. The primary prey was zooplankton in the order Cladocera, commonly called water fleas. The compatibility, on the same farm fields, of summer crop production and native fish habitat during winter demonstrates that land management combining agriculture with conservation ecology may benefit recovery of native fish species, such as endangered Chinook salmon.

Flows and Fishes in the Sacramento-San Joaquin Delta

Delta Stewardship Council (Delta Council) | August 1st, 2015

Record-low counts of Delta smelt at a time of persistent drought underscore the importance and challenges of managing freshwater flows for the benefit of fishes in the Sa

Record-low counts of Delta smelt at a time of persistent drought underscore the importance and challenges of managing freshwater flows for the benefit of fishes in the Sacramento-San Joaquin Delta while also meeting human demands for water. Understanding the effects of water flows on fishes is central to understanding how the Delta ecosystem functions and is key to achieving the state’s coequal goals of “providing a more reliable water supply for California and protecting, restoring and enhancing the Delta ecosystem … in a manner that protects and enhances … the values of Delta as an evolving place”. The economic, ecological, and social costs of scientific uncertainty in water management controversies are significant - and to some degree unavoidable. Scientific findings that relate fishes and flows increasingly guide decisions on how to manage flows for the well-being of threatened or endangered species in the Delta. Many studies – and management decisions – rely on correlations between water flows and fish populations. But the decisions warrant fuller understanding of precisely how the flows affect the fishes. Knowledge of these underlying mechanisms is likely to facilitate adaptive management by clarifying uncertainty and risk, by creating specific expectations for outcomes and by strengthening testable hypotheses. This report therefore recommends, first and foremost (there are other recommendations as well), redoubling effects to identify causes and effects concerning fishes and flows in the Delta.

Food Web Fuel Differs Across Habitats and Seasons of a Tidal Freshwater Estuary

Estuaries and Coasts (Springer) | July 11th, 2020

Estuarine food webs are fueled by multiple different primary producers. However, identifying the relative importance of each producer to consumers is difficult, particula

Estuarine food webs are fueled by multiple different primary producers. However, identifying the relative importance of each producer to consumers is difficult, particularly for fishes that utilize multiple food sources due to both their mobility and their generally high trophic levels. Previous studies have documented broad spatial differences in the importance of primary producers to fishes within the Upper San Francisco Estuary, California, including separation between pelagic and littoral food webs. In this study, we evaluated the importance of primary producers to adult fishes in three closely spaced subregions that represented disparate habitat types (a tidal wetland channel, a turbid backwater channel, and a deep open-water channel), each a potential outcome of local restoration projects. Using stable isotope analysis coupled with a Bayesian mixing model, we identified significant differences in primary-producer contribution to fishes and invertebrates across habitats and seasons, especially in the relative contribution of submersed aquatic vegetation and phytoplankton. Most fishes utilized multiple primary producers and showed little segregation between pelagic and littoral food webs among habitats. Availability of primary producers differs seasonally and across multiple spatial scales, helping to buffer environmental variability and thus enhancing food web resilience. Ecosystem restoration may improve with emphasis on restoring a wide variety of primary producers to support consumers.

Food Webs of the Delta, Suisun Bay, and Suisun Marsh: An Update on Current Understanding and Possibilities for Management

University of California, Davis (UC Davis) | October 1st, 2016

This paper reviews recent research findings on food web processes since 2008. It also highlights the idea of a changing baseline with respect to food web function. New re

This paper reviews recent research findings on food web processes since 2008. It also highlights the idea of a changing baseline with respect to food web function. New research indicates that interactions between habitat-specific food webs vary across the current landscape. For example, based on early work in the south Delta, the food web associated with underwater vegetation was thought to provide little support to species of concern; however, data from other regions of the estuary suggest that this conceptual model may not apply across the entire region. Habitat restoration has been proposed as a method of re-establishing historic food web processes to support species of concern. Benefits are likely for species that directly access such restored habitats, but are less clear for pelagic species. Several issues require attention to further improve the knowledge of food webs needed to support effective management, including: (1) synthesis of factors responsible for low pelagic biomass; (2) monitoring and research on effects of harmful algal blooms; (3) broadening the scope of long-term monitoring; (4) determining benefits of tidal wetland restoration to species of concern, including evaluations of interactions of habitat-specific food webs; and (5) interdisciplinary analysis and synthesis. The only certainty is that food webs will continue to change in response to the changes in the physical environment and new species invasions.

Fortresses of mud: how to protect the San Francisco Bay Area from rising seas

Nature Portfolio (Springer Nature) | October 9th, 2018

There’s something apocalyptic about this pond on the east side of San Francisco Bay, California. The legacy of a salt industry that has moved elsewhere, it has subsided

There’s something apocalyptic about this pond on the east side of San Francisco Bay, California. The legacy of a salt industry that has moved elsewhere, it has subsided a couple of metres below the level of neighbouring marshland. Algae paints red swirls in the brown water, and the pond’s edge is crusted hard with sparkling salt. As a breeze eases off the bay, a squadron of pelicans sails by, en route to more-appetizing hunting grounds. But there is a better future ahead for landscapes like this one in the Eden Landing Ecological Reserve and elsewhere around the bay. Over the next decade, government officials plan to fill many such depressions with sediment and then open them up to the tides. Eventually, cordgrass, pickleweed and other marsh vegetation will take root, restoring this crucial marsh ecosystem. The goal is to try to create a natural buffer to protect the heavily populated waterfront, by sapping energy from storm surges and blocking the highest tides.

Framework to Coordinate Water Quality Improvement and Wildlife Habitat Conservation to Protect California Streams, Wetlands and Riparian Areas

San Francisco Estuary Institute (SFEI) | February 1st, 2016

The emergence of comparable landscape approaches to wildlife conservation and water quality improvement through federal and California state regulatory and management pr

The emergence of comparable landscape approaches to wildlife conservation and water quality improvement through federal and California state regulatory and management programs provides an opportunity for their coordination to better protect California’s aquatic resources, especially streams, wetlands, and riparian areas. Such coordination is patently desirable. A framework has been developed to help coordinate restoration and compensatory mitigation across policies governing wildlife conservation and water quality in the landscape context. The framework is based on the Wetland and Riparian Area Monitoring Plan (WRAMP) of the California Wetland Monitoring Workgroup (CWMW) of the Water Quality Monitoring Council. The framework presented here is a version of the standard WRAMP framework. It only differs from the standard framework to better accommodate wildlife conservation planning, assessment and reporting. To distinguish this version from the standard version, it is termed theWRAMP for wildlife (WRAMPw).

Franks Tract Futures

Delta Stewardship Council (Delta Council) | April 26th, 2022