State of the Estuary Report 2019

Report & Summary


Appendices & Credits

State of the Estuary 2019

Status and Trends of Indicators of Ecosystem Health

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State of the Estuary Status and Trends Cover

The projects we manage and the people and species they affect are all one, and we must recognize and work through the complexities. It will take much more than measures of acreage, elevation, and access to sustain California’s ecosystems and residents in the future.

Caitlin Sweeney


We need more investment in creative ways to use and restore flows for environmental health, to expand and build resilient shorelines with rising land elevations, and to weave considerations of social equity more strongly into efforts to improve environmental health.

Letitia Grenier

Lead Scientist

Executive Summary

Read the Executive Summary in your browser, download, or print it.

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Health Indicators

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.

Updated Indicators

A look at five central measures of Estuary health — freshwater flow, tidal marsh extent, native fish communities, beneficial flooding, and how much water humans use in urban areas.

Freshwater Flows

Freshwater flows in the Estuary have been highly altered, causing reductions in inter-annual and seasonal variability, and peak-flows. Freshwater flows into the Estuary in recent years reflect chronic artificial drought conditions, which is in sharp contrast to historic unimpaired flows.

Tidal Marsh

Tidal marsh acreage throughout the Estuary has declined significantly from historic records, but restoration efforts are bringing back this critical ecosystem and its associated benefits. Projects in the Bay are making extensive contributions to tidal marsh acreage, while efforts in the Delta are beginning to make progress towards regional goals.

See clips from an interview with Letitia Grenier, PhD (San Francisco Estuary Institute), science lead and co-author of the updated indicator on tidal marsh for the 2019 State of the Estuary Report.


The condition of fish communities varies across the Estuary. In the lower Estuary, fish communities are abundant, diverse, and dominated by native species. However, based on long-term monitoring data, native fish communities in the Bay are declining. In San Francisco and San Pablo Bays, this long-term data set is from sampling only the offshore areas of the Bay and may not reflect benefits to fish populations from recent wetland restoration. In the brackish and freshwater upper Estuary, native fish communities are in poor condition.

See clips from interviews with Christina Swanson, PhD (Natural Resources Defense Council) and Jon Rosenfield, PhD (San Francisco Baykeeper), co-authors of the updated indicator on Bay and Delta fish for the 2019 State of the Estuary Report.

Beneficial Floods

The frequency, magnitude, and duration of floodplain inundation in both the Bay and the Delta are too low to support healthy estuarine habitats and sustain important ecological processes. While conditions have been variable over time, they have, in general, remained poor in the Delta and have declined in the Bay.

Urban Water Use

In both the Bay and Delta, total and per-capita urban water use have declined over the last several decades, despite growing populations. More efficient urban water use means that both regions met and exceeded benchmarks for per-capita use and drought-reduction targets. The regions have modestly increased water use since the end of the drought but still maintained improvements over their 2020 benchmarks for reductions in per-capita use.

See clips from an interview with Peter Vorster (The Bay Institute), co-author of the updated indicator on urban water use for the 2019 State of the Estuary Report.

Emerging Indicators

The 2015 State of the Estuary Report developed three cutting-edge indicators of Estuary resilience.  These indicators offer vital, science-based insights into the frontiers of Estuary management. In the future, these indicators will be refined with additional input from scientists and stakeholders to identify appropriate datasets, approaches, and benchmarks for meaningful and replicable monitoring and management.

Subsided Lands

Significant portions of previously tidal areas in the Bay and Delta have been diked off and disconnected from tidal action to accommodate agriculture, urban development, duck ponds, salt ponds, and a diverse set of other land uses. The low elevation of these areas places them at increased risk of flooding as sea level rises and intense rainstorms become more common. In addition, many of these former tidal marshes and mudflats have subsided significantly below sea level as a result of sediment oxidation and compaction. Subsidence and these accompanying processes exacerbate flood risk, contribute to greenhouse gas emissions, and reduce the potential for restoring important intertidal habitat types.

Shore Resilience

Levees and seawalls line many miles of shorelines along the San Francisco Bay and the Sacramento-San Joaquin Delta. By hardening the Estuary’s once soft and absorbent shores, early developers intended to keep people and property safe from flooding; however, These engineered structures do not provide good habitat for native species. These structures were also not designed to accomodate flooding projected for our future, which includes a combination of rapid sea level rise, higher groundwater tables, storm surge, and more rainfall over shorter periods.

Urban Green Space

Open spaces within urban areas provide a diverse set of benefits for wild animals, plants, and people that live nearby. Green spaces decrease urban runoff, improve downstream water quality, and provide habitat for native wildlife, while also benefiting human health and wellbeing. Urban parks improve local air quality and reduce local temperatures, contributing to lowered rates of childhood asthma and heat-related deaths in nearby areas. Exposure to urban parks is also associated with improved mood, increased physical activity, lower heart rate, and additional human health benefits.


Technical Appendices

Review the technical materials associated with this report that were gathered, produced, and reviewed by subject-matter experts.

Download the Combined Technical Appendices for the 2019 State of the Estuary Report

Credits and Acknowledgements

Science Coordination

April Robinson,
San Francisco Estuary Institute

Science Lead

J. Letitia Grenier,
San Francisco Estuary Institute

Contributing Scientists

Freshwater Flows

Christina Swanson,
Natural Resources Defense Council

Beneficial Floods

Christina Swanson,
Natural Resources Defense Council

Tidal Marsh Extent

Emily Clark,
Sam Safran,
San Francisco Estuary Institute


Christina Swanson,
Natural Resources Defense Council

Jon Rosenfield,
The Bay Institute/Bay Keeper

Bill Bennett,
The Bay Institute

Urban Water Use

Peter Vorster,
Greg Reis,
The Bay Institute

Urban Green Space

Matt Benjamin,
Sam Safran,
Erica Spotswood,
San Francisco Estuary Institute

Nature-based Shorelines

Katie McKnight,
Sam Safran,
Julie Beagle,
San Francisco Estuary Institute


Matt Benjamin,
Sam Safran,
San Francisco Estuary Institute

Steering Committee

Caitlin Sweeney,
Liz Juvera,
San Francisco Estuary Partnership

Martina Koller,
John Callaway
Delta Stewardship Council

Luisa Valiela,
U.S. Environmental Protection Agency


Ariel Rubissow Okamoto,
Lisa Owens Viani

VOICES sections draw from ESTUARY News Magazine stories with additional research by Aleta George and Audrey Mei Yi Brown.


Miguel A. Osorio, Layout Design
Peter Beeler, Estuary Map
Metropolitan Transportation Commission


JT Litho,
Oakland, California
Printed on Recycled Paper

Online Materials

Tony Hale,
San Francisco Estuary Institute

Cover Photos

Left to right: Shira Bezalel; Don Yee; Shira Bezalel; Ken James

Website Video

Andy Miller,
Plus M Productions


This report was funded by the San Francisco Estuary Partnership and the Delta Stewardship Council.

We would like to thank the many people who contributed to the development and review of this report, including: Ruth Askevold, Josh Bradt, Gary Bobker, Amanda Bohl, Josh Collins, Will Dominie, Liz Duffy, Cristina Grosso, Kathy Hieb, Nahal Ipakchi, Jessica Law, Jeremy Lowe, Darcie Luce, Ron Melcer, Thomas Mumley, Heidi Nutters, Ellen Plane, Sandra Scoggin, Tim Smith, and Christina Toms.