State of the Estuary 2019 Update

San Francisco Estuary Partnership (SFEP) | October 22nd, 2019

The San Francisco Estuary is a large and diverse system. Hundreds of miles of coastline stretch from the wide valleys of the Sacramento and San Joaquin Rivers to the stee

The San Francisco Estuary is a large and diverse system. Hundreds of miles of coastline stretch from the wide valleys of the Sacramento and San Joaquin Rivers to the steep headlands of the Golden Gate, with vast agricultural fields in the Delta and urbanized shorelines in Silicon Valley and many of the region’s cities. The complexity and scale of this system means it can take years to detect and assess changes. This interim State of the Estuary Report checks in on a few indicators of health and explores where the assessment should head over time. In the four years since the 2015 State of the Estuary Report, two issues have emerged as critical to how we assess the health of the estuarine ecosystem at the heart of the Bay Area and the Delta. First, the health of the Estuary and of the people who live near it and depend on it are inextricably linked. We need a healthy Bay and Delta to protect our shorelines from sea level rise, help keep our waters clean, provide food and habitat for fish and wildlife, and give people a place to enjoy nature. We also need to think more about human communities as we assess the health of natural communities. This focus means addressing environmental injustices that are deeply embedded in our culture and patterns of development. The second critical issue to emerge is the need for a greater focus on landscape resilience—how well the Bay and the Delta are equipped to respond to change—so that people and wildlife can thrive as climate change progresses. Taking these two ideas together, this report focuses on the nexus of social and ecological resilience as we look toward the future. The first section of the Report updates indicators of ecological health that span the entire extent of the San Francisco Estuary (Bay and Delta). Recent data show continued progress along the trajectories of the past decade. Tidal marsh restoration is proceeding at a brisk pace in the Bay and gaining traction in the Delta, while urban water conservation continues to meet mandated benchmarks, even during the drought. On the other hand, flows through the Estuary and across its floodplains continue to be well below levels that could increase and restore ecosystem health. Freshwater flows are a lynchpin of ecosystem processes that sustain physical habitats, fuel the food web, and regulate water quality. Creative approaches to using and re-using fresh water for environmental purposes are needed. Long-term trend analysis shows that fish communities in the Bay are declining. This analysis scores an index of 10 attributes of a healthy fish community. The index focuses on fish in offshore areas, and may not capture benefits to fish from near-shore wetland restoration projects. Despite this slow decline, fish communities in the saltier parts of the Estuary remain in good condition, while those in the brackish and freshwater areas are in poor condition. The next section of the report discusses three emerging indicators of Estuary health, offering options for how to assess resilience in future reports. Here, for the first time, the resilience of the Estuary’s shores is evaluated through the lens of subsidence and nature-based features. Elevation relative to sea level is a basic currency that must be tracked as the Pacific Ocean rises into the Estuary. The potential for the Estuary shore to be resilient to climate change and continue to provide benefits to people is related to how much of the shore zone is nature-based. The final emerging indicator, urban green space, is a first attempt to assess how access to nature is distributed across more and less advantaged communities. More work is needed to finalize all these emerging indicators before they can be included in any future quantitative assessment of the State of the Estuary. These emerging and updated indicators will help focus efforts to restore the Estuary’s health. In addition to continuing the successful aspects of restoration and conservation that this report describes, we need more investment in creative ways to use and restore flows for environmental health, to expand and build resilient shorelines and to weave considerations of social equity more strongly into efforts to improve environmental health. - J. Letitia Grenier, Lead Scientist

Status and trends of dam removal research in the United States

Wires Water (Wiley) | September 6th, 2016

Aging infrastructure coupled with growing interest in river restoration has driven a dramatic increase in the practice of dam removal. With this increase, there has been

Aging infrastructure coupled with growing interest in river restoration has driven a dramatic increase in the practice of dam removal. With this increase, there has been a proliferation of studies that assess the physical and ecological responses of rivers to these removals. As more dams are considered for removal, scientific information from these dam‐removal studies will increasingly be called upon to inform decisions about whether, and how best, to bring down dams. This raises a critical question: what is the current state of dam‐removal science in the United States? To explore the status, trends, and characteristics of dam‐removal research in the U.S., we searched the scientific literature and extracted basic information from studies on dam removal. Our literature review illustrates that although over 1200 dams have been removed in the U.S., fewer than 10% have been scientifically evaluated, and most of these studies were short in duration (<4 years) and had limited (1–2 years) or no pre‐removal monitoring. The majority of studies focused on hydrologic and geomorphic responses to removal rather than biological and water‐quality responses, and few studies were published on linkages between physical and ecological components. Our review illustrates the need for long‐term, multidisciplinary case studies, with robust study designs, in order to anticipate the effects of dam removal and inform future decision making

Still Imperilled, Still Important: The Little Hoover Commission’s Review of the CALFED Program

Little Hoover Commission | November 17th, 2005

The Sacramento-San Joaquin River Delta is a treasured and imperiled resource. And CALFED has been the best hope to restore it. The ambitious state-federal partnership is

The Sacramento-San Joaquin River Delta is a treasured and imperiled resource. And CALFED has been the best hope to restore it. The ambitious state-federal partnership is proof that political will and leadership can resolve seemingly intractable conflicts. And yet in recent years, the program also has demonstrated the propensity for rudderless bureaucracies to get caught in inescapable eddies. It is not too late for the Delta, or for CALFED. But restoring the estuary and managing the resource in a sustainable manner will require continuous political support, expert leadership, and smart management.

Strategies for Managing the Colorado River in an Uncertain Future

Utah State University | January 11th, 2020

Colorado River managers and stakeholders face many uncertainties—issues such as climate change, future water demand, and evolving ecological priorities. Managers and st

Colorado River managers and stakeholders face many uncertainties—issues such as climate change, future water demand, and evolving ecological priorities. Managers and stakeholders are looking for new ways to communicate about uncertain future conditions, help cope with an uncertain future, and develop public policy when future conditions are highly uncertain. Historically, Colorado River managers have operated Lake Powell and Lake Mead under the assumption that the future natural flow regime of the Colorado River at Lee Ferry will resemble the previously observed regime, but most climate scientists believe that the flow regime is changing, and that future flows will be lower, more variable, and more uncertain.

Stream Flow and Losses of the Colorado River in the Southern Colorado Plateau

Utah State University | September 18th, 2020

A confounding uncertainty for predicting stream flow and losses in anticipation of renegotiation of the 2007 Interim Guidelines for Lower Basin Shortages concerns the acc

A confounding uncertainty for predicting stream flow and losses in anticipation of renegotiation of the 2007 Interim Guidelines for Lower Basin Shortages concerns the accuracy and precision of those data. Several key gages that are not used in CRSS and are not considered part of the standard network of gages used to manage the Colorado River offer critical insight into understanding future watershed conditions.

Survey Fishes: An Illustrated List of the Fishes Captured during the Northwest Fisheries Science Center’s Fishery Resource Analysis and Monitoring Division’s West Coast Survey

National Marine Fisheries Service (NMFS) | September 1st, 2017

The intention of this guide is to be a field reference to the fishes captured during the various Fishery Resource Analysis and Monitoring Division (FRAM

The intention of this guide is to be a field reference to the fishes captured during the various Fishery Resource Analysis and Monitoring Division (FRAM) West Coast surveys. Scientific and technical terms have been kept to a minimum and, when used, are defined within the text. Descriptions and distribution are confined to those species within the geographic (U.S.–Canada to U.S.–Mexico borders) and depth (30–1,680 m) parameters of the FRAM West Coast surveys. Many of the fishes described have geographic and/or depth ranges that extend outside of the survey parameters. Distributions include these areas and are described by political boundaries (e.g., state and/or country borders), bodies of water (i.e., the northeastern Pacific, the Strait of Juan de Fuca, the Columbia River, etc.), islands and/or major geographical features (i.e., the Hawaiian, Farallon, and Channel Islands, Cape Flattery, Point Conception, etc.). Conducted aboard small commercial vessels with limited personnel and space, the majority of the FRAM West Coast surveys do not have access to wet/dry lab facilities for detailed observations. Due to a variety of factors such as body size and specimen damage, internal meristic counts (i.e., vertebrae or pyloric caeca), and others that cannot be made with the naked eye, identification of some groups of fishes included in this text are treated only to the family or generic level. The species accounts are in scientific order as much as possible. The list of common and scientific names are in the List of Species. Photographs are provided when available. The family and species keys are for the families/species within the guide. However, some species not known from within the scope of this work may have been included to complete a couplet.

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.

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.

The Delta as Changing Landscapes

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

What happens at one place in a landscape influences and is influenced by what happens in other places. Consequently, management and restoration that focus on individual p

What happens at one place in a landscape influences and is influenced by what happens in other places. Consequently, management and restoration that focus on individual places may fail to recognize and incorporate interactions across entire landscapes. The science of landscape ecology, which emphasizes the interplay of landscape structure, function, and change at multiple scales, offers a perspective that can integrate the spatial relationships of ecological processes and the functional interconnections of land and water in the Delta. Although the Delta is one of the most studied estuaries in the world, applications of landscape science have been limited. We describe why it is important to incorporate landscape science into management and restoration, emphasizing how Delta landscapes have changed over the past centuries. The land–water linkages of the past have been broken, waterways have been over-connected, and hard boundaries have replaced the gradual and dynamic transitions among landscape patches. The contemporary landscape also has new, novel assemblages of species and stressors that were not there in the past. This historical perspective indicates how knowledge of past landscape functions can contribute to the restoration and management of contemporary landscapes. We illustrate these points with case studies of inundation dynamics and riparian woodlands, and use a third example to describe a landscape approach to restoration. We propose that science that encompasses the multiple, interacting components of functional landscapes in the Delta will foster resilient and enduring restoration and management outcomes that benefit both people and wildlife. We suggest several ways of moving landscape science to the forefront of management and restoration in the Delta.

The effects of aquatic area abundance, buffer, and hydrology on depressional wetland condition based on CRAM

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