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DELTA STEWARDSHIP COUNCIL: Briefing on the 2019 update to the State of the Estuary Report

San Francisco Bay by Gordon

The San Francisco Estuary Partnership periodically reports on the health of the estuary, producing the State of the Estuary report which assesses the status of various parameters of the ecosystems of both the San Francisco Bay and the Sacramento-San Joaquin Delta and summarizes the latest scientific findings about ecosystem health. The State of the Estuary report is the only place where a holistic view of ecosystem function is provided across both the Bay and the Delta. The objective of the report is to identify problems with estuarine health so that conservation and restoration efforts can focus on solutions.

At the December meeting of the Delta Stewardship Council, Caitlin Sweeney, Director of the San Francisco Estuary Partnership, briefed the Council on the 2019 update to the State of the Estuary report.  She began with some background on the Partnership.

The San Francisco Estuary Partnership was established in 1988 by the State of California and the U.S. Environmental Protection Agency under the Clean Water Act’s National Estuary Program at the time the San Francisco Estuary was designated as an estuary of national significance under the US EPA’s Clean Water Act.  The San Francisco Estuary Partnership manages important multi-benefit projects that improve the health of the Estuary by building partnerships and leverage federal funding with millions of dollars in state and local funds for regional-scale restoration, water quality improvement, and resilience-building projects.

The map shows the extent of their planning area, which includes the San Francisco Bay and the Sacramento-San Joaquin Delta.  The Partnership is a federal, state, and local partnership; their fiscal and administrative home is with the Association of Bay Area Governments who recently merged with the Metropolitan Transportation Commission.  The Partnership is guided by a 38-member implementation committee, which includes representatives from local, state, and federal agencies, businesses, and environmental organizations.

One of the responsibilities of the partnership is to track and report out on the health of the estuary.  The State of the Estuary reports are comprehensive health reports for the entire estuary that relies on best available science and recent data to assess the status and the trends of various parts of the ecosystem.


In October, the Partnership released the 2019 update to the State of the Estuary report, which focused on the idea that the health of the estuary and the health of the people who live near it, recreate around it, and depend upon it are linked, and that a much greater focus is needed on landscape resilience so that the Bay and Delta will be equipped to respond to future climate change.

The San Francisco Estuary is a very large and diverse system, and the complexity and scale of the system means that it can take years in some cases to detect change.  The 2015 State of Estuary report had 32 indicators of change; for the update, they updated five of the indicators that were estuary-wide.

We wanted to talk about how the entire estuary was doing as a system, so we focused on these five indicators where the data that we had available could detect some change and frankly where we could tell a story,” said Caitlin Sweeney.

The color of the indicator on the scorecard is the status of the indicator, which is good (green), fair (yellow), or poor (red).  An arrow pointing up indicates improving, an arrow pointing down indicates declining, and a diamond indicates mixed results.

Ms. Sweeney began with some positive stories, beginning with tidal marsh restoration, which is proceeding at a brisk pace in the Bay and gaining traction in the Delta.

I think this really reflects an understanding of our entire region as to the urgency of our need to restore our tidal marsh ecosystems and restore them at a pace and scale that will benefit us as we are facing impacts from sea level rise,” she said.  “So although the status of the Bay and Delta with regard to acreage isn’t exactly where we’d like to see it, the trend is very much improving for both.  It’s a real shift in the trend from five years ago that was happening in the Delta.”

The other positive story is with regard to urban water use and water conservation.  The major urban areas in both the Bay and the Delta met and exceeded mandated water conservation measures during the drought years, and post-drought even when those conservation measures are no longer mandated, the behavior is being maintained.

We’re still seeing that same behavior change, and we’re still using much less water then we were prior, so this shows is our ability again as a community to change our behavior in response to crisis and then really keep that behavioral change even post crisis,” she said.

However, freshwater flowing into the estuary from rivers and streams has been highly altered and freshwater flows are critical for ecosystem processes.

The estuary is still experiencing what we term to be a chronic drought relative to what we might see if flows were completely unimpaired into our system,” she said.  “So the status of this indicator is poor and the trend is still declining throughout the estuary.”

It is a similar story with regard to beneficial floods, she said.  “Water flowing across floodplains, across the estuary and into the Delta and Bay are also important drivers of ecological processes, and that beneficial floods continue to be well below the frequency and the magnitude and the duration that we need to increase to restore ecosystem health.   So in other words, we still need to give rivers more room to roam and move, and we need to think about releasing water from dams at strategic points.

The fish story is more complex where in the upper estuary, fish communities are in poor condition in most of the subregions and the trends are mixed.

The state of the communities really reflects the long-term decline that we’ve been witnessing, as well as the more short term adverse conditions from recent drought and related actions,” she said.  “The exception to the overall trend in the upper estuary is in Suisun Marsh, where the relative percent of native fish have showed an improvement over the past 5 years.”

Ms. Sweeney noted that in the lower estuary, while the overall status is good, the long-term trend analysis actually shows that fish communities are declining.

What is interesting about that is that this is based on a 38 year data set, so it’s taken us 38 years to be able to detect that long-term trend, showing again the importance of being able to collect and track those trends over a long period of time,” she said.


The report also introduces three new emerging indicators of estuary health; these indicators are forward-thinking and trying to discover new ways of measuring resilience to capture it in the report.  So for the update, they chose and worked out three new emerging indicators of landscape and community resilience.

Subsided lands

This indicator represents the idea that the resilience of the estuary shores can be evaluated through the lens of subsidence by tracking the elevation related to sea level over time.

Significant acreage of previously tidal areas of the Bay and Delta have been diked off and disconnected from tidal action to accommodate development and agriculture.

Across the estuary, there are about 400,000 acres of land at intertidal or subtidal elevations that are now disconnected from the tides, which is interesting, because that is actually a larger area than the acreage that is connected to the tides or influenced by tides on an everyday basis,” Ms. Sweeney said.  “About three quarters of those low lands are located in the Delta region.  The low elevations of these areas places them at increased risk of flooding as sea level rises and rains become more intense.  As sea levels rise and lands continue to subside, flooding from creeks and groundwater will become more prevalent, and greater intervention will be needed to maintain and protect land uses behind these areas.  Of course there are many areas behind these levees that offer us great opportunities to restore land to tidal action and we’re seeing that throughout the estuary as well.

Future iterations of this analysis will help gauge how well wetland restoration and other interventions like sediment augmentation can change elevations in the region and enhance resilience.

Shoreline resilience

The next emerging indicator is another way to measure shore resilience.  Levees and seawalls have hardened much of the estuary’s once soft and absorbent shores, and these levees and seawalls not only don’t provide good habitat for native species but also in many cases aren’t designed to accommodate projected future flooding, she said.  So the potential for the estuary shore to be resilient to climate change and continue to provide benefits to people is very tied to how much of the shoreline is nature based or has some sort of natural element to it.

For the report, they evaluated shore resilience based on mapping the shore type all around the estuary.  “We found that in the Bay, more than half of the shore supports some sort of natural or managed wetland that can help facilitate resilience, but in the Delta, only 13% of the shore supports these ecosystems,” Ms. Sweeney said.  “So over time this indicator could track management actions to protect communities and land uses using adaptation strategies that includes nature-based adaptation.”

As this indicator is refined in future iterations, it will be important to keep in mind the differences between the Bay and the Delta.  In the Bay, much of the shore is located on the end edge and includes an area for transition to upland areas whereas in the Delta, much of the shore is leveed channels bordering subsided lands, so different types of nature-based strategies will be more appropriate, feasible, and successful in different areas in the estuary.

“Whereas in the Bay, we might focus on beach restoration or restoring subtidal oyster reefs, in the Delta, we might focus on wetland restoration to halt subsidence and regain elevation,” she said.

Councilmember Ken Weinberg asks about land use conflicts in the Bay.  The differences between the land use on the edges of the Bay and in the Delta are quite different and not comparable, he says.

Ms. Sweeney said that there is a fairly good understanding in the Bay of where the opportunities are for nature-based solutions, including where there might be willing collaborations with adjacent land uses and landowners.

We’re also finding an understanding of the benefits of nature-based solutions regardless of the adjacent land use,” she said.  “We can really provide increased resiliency along with cobenefits, with habitat, with recreational opportunities, with better aesthetics, and these are strategies that are much cheaper to maintain over time than a levee or a seawall, although clearly there are areas where a levee or a seawall is the only option.”

Green space

The last emerging indicator is urban green space.  They want to track community resiliency and equity, and since access to green space and nature is related to human health benefits, such as improving air quality, reducing local temperatures, increasing mental well-being, and providing opportunities for exercise and recreation, so the report analyzes park and population distributions together to determine how equitably people benefit from parks.

Most urban areas around the estuary exceed the national average in terms of park access, so we do a pretty good job in increasing and providing green space to our residents,” said Ms. Sweeney.  “However, the amount of accessible land varies and in disadvantaged communities, parks tend to be smaller with more potential users nearby than in other areas.  So an indicator like this would allow us to track changes in public access to green space over time with this lens of equity.”

Voices of the Estuary

For the report, they wanted to hear from people around the estuary, such as those that recreate in and around the estuary, landowners who choose to restore their creeks or improve water quality in addition to their other land uses, and those who are working to weave environmental justice and racial equity into environmental management.

We know that many of the same drivers that put the health and the function of the estuary at risk have also placed certain communities at risk and that the impacts of impaired estuarine health are not felt equally,” she said.  “Whether we’re talking about rising seas, quality of drinking water, health of the fish that people eat, or proximity to open space, so as communities really lead the way in this arena and government agencies such as mine build our skills to partner and collaborate, I do see that solutions are emerging that work to address historical patterns of injustice.  We know essentially that we can’t restore the ecological health without restoring our social fabric and addressing this history of past injustices.”


The State of the Estuary Report drives the regional actions taken by the Partnership and their partners to increase the health and resilience of the estuary.

One of the take home messages of the report is that we need to continue to invest in restoration,” Mr. Sweeney said.  “We’re doing a great job but we need to continue to do that and increase the pace and scale of our restoration efforts.  We see that behavior can change and that is a sustainable change and continuing to find ways to change and support behavior change.  Clearly a continued focus is needed on restoring freshwater flows to our system and expanding and rebuilding resilient shorelines.

We’re looking for opportunities and making room to weave social equity more strongly into our efforts to improve the health of the environment, and we’ll continue to monitor and report out on these changes over time.  We know that resilience is not rebuilt or regained overnight, and those of us engaged in reporting on it, analyzing it, responding to these challenges really need to, as we say, ‘stick it up and step it up’.

The full report is available by clicking here.

Councilmember Oscar asks if there are distillable aspects of the report that can be embedded in practices or ideas or principles that can be used at the Stewardship Council.  Are there things we should be thinking about?

The key thing that we’ve been trying to think about is functional flows and how can we most effectively use the water that is available,” said Lead Scientist Dr. John Callaway.  “I think the voluntary agreements will be where there’s hopefully some opportunities to improve the way that we are managing flows and using flows for ecosystem benefits and then connecting that to restoration.  It’s not just flows alone; it’s a combination of flows and restoration and linking the beneficial floods and floodplain inundation, to me that’s where it’s really critical.  In terms of actionable issues, I would say putting more effort and thought into how we jumpstart restoration which I think the ecosystem amendment is really pushing hard on that, connecting that to flows, and then the last thing is connecting it to social issues that I think is a key part of what the report is all about.  In that regard, the draft social science plan is going to come out which is our biggest effort to get traction in that area and to raise the awareness and importance of social issues and to get more research moving in that regard.”

Letitia Grenier acknowledged that from a Delta perspective, the report can seem very negative.  “I just want to remind everybody that when we see examples of change happening in the Delta, the ecosystem responds, so my sense of it is it’s not an ecosystem that’s so far gone that our actions can’t achieve results just as they are achieving them in the Bay.  We’ve seen some examples of pilot attempts to create floodplain inundation, and the way that the Yolo Bypass is being managed is changing, and those are really effective management actions, and I think that thing that needs to be done is just increasing the pace of making those kinds of things happen.  There certainly are the political challenges, but on the ecological side, there are actions that are very doable that could be very effective, and I want everyone to remember that because things can look negative in the Delta, but it’s very baked in to the direction that you’re going with the Delta Plan and the ecosystem amendment.”


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