By Guananí Gómez-Van Cortright & Ariel Rubissow Okamoto
In 1999, regional managers vowed to restore 100,000 acres of tidal wetlands in the San Francisco Estuary by 2030. More than two decades later, over 53,000 acres have been or are in the process of being restored. But the effort to track those acres, and monitor the success of tidal marsh restoration projects, has relied on a patchwork of data collection efforts, each using different sampling methods over different time scales. Managers are still often unclear on whether these wetlands are flourishing or providing good habitat for target fihs, birds and mammals.
“We know very little about many of these habitats; they’ve just never been sampled in a standardized way,” says Levi Lewis, UC Davis fish ecologist.
Six years in the making, an effort to close these gaps is finally gaining traction. Early in 2025, the Wetlands Regional Monitoring Program began to put more crews in the field, sensors in the ground, and links in the public access EcoAtlas map to regularly track changes in the Bay’s wetland ecology from Silicon Valley to Suisun Bay. The program will also link all this monitoring to similar efforts in the Delta, where about ⅓ of the estuary’s current wetlands can be found, and where nearly all the monitoring expertise and resources have been focused historically.
“It’s a collaborative regional monitoring program that aims to improve wetland restoration across the whole San Francisco Estuary,” says Aviva Rossi, a lead scientist with the WRMP.

The project is co-managed by the San Francisco Estuary Institute and Estuary Partnership, and funded for the next two years via the San Francisco Bay Restoration Authority and US EPA. The program will work to establish a regional dataset that can elevate estuarywide science and enable researchers and managers to compare how different wetlands are changing under the influence of restoration projects, as well as in response to sea level rise, drought, and other environmental shifts.
“The WRMP will standardize what is collected and how it’s collected so that you can get a more unified assessment of how these sites are changing over time,” says Lisa Beers, also a lead scientist with the WRMP. “[We’ll] know that any changes we see in the extent of wetlands over time are due to actual management actions and restorations, rather than differences in methodology or how the mapping was done.”
Eyes on the marsh
The mosaic nature of estuary and especially wetland monitoring have made communicating between agencies and securing reliable sources of funding a major challenge for decades. Programs like the Interagency Ecological Program in the Delta, and the Regional Monitoring Program for contaminants in San Francisco Bay, have long sought to coordinate, share and optimize research and monitoring endeavors — but it isn’t easy.
“Since we don’t have any central governing agency that’s effective from the coastal ocean to the headwaters, you have to piecemeal this stuff together from existing programs across, in [our] case, nine agencies, and we don’t always get it right,” says Steve Culberson, lead scientist at the Interagency Ecological Program and program manager with the Delta Stewardship Council Delta science program.

Combining existing surveys of the Delta — many focused on fish and water-quality sampling — with new monitoring of recently restored habitats has proven difficult. While fish and birds can move freely between project sites, information can’t.
Many existing monitoring programs are tied to specific management questions, or to specific restoration sites designed to mitigate impacts from a specific development or water diversion project. Often, that kind of monitoring can be patchy, project-centric, and short-lived, as most permits require just two to five years of sampling.
“The WRMP is different in that it’s regional and long-term,” says Rossi. “The scope and scale involves coordinating across a big area with multiple jurisdictions and players, as well as supporting project-based efforts and making them more efficient and less costly. That’s all really challenging to pull off, which is why it’s taken decades to get to this moment.”
The WRMP will collect samples in previously understudied areas in the South, North, and Suisun Bays, such as Eden Landing, Ravenswood, Galinas, Novato, and the Petaluma and Napa River systems. The same consistent, trackable, repeatable methods will be used to collect metrics across sites and regions, and over seasons and years. This January, for example, a field crew established some new long-term vegetation transects (a set line across the marsh where plant growth is measured), placed new piezometers in the ground (which measure groundwater rise), and re-instated some sediment accumulation sensors to better align with the stepped-up monitoring effort, among other efforts that will help pin down baseline conditions of wetlands.
Future sampling will collect data on a suite of metrics to judge the health and functioning of wetlands, including water quality metrics such as temperature, salinity, and dissolved oxygen. Habitat assessments will track vegetation cover, biodiversity, and fish species abundance as they change over time due to climate change, development, runoff and sea level rise. Data collected as part of the project will be publicly available on an online data portal, as well as in published reports.
“People are excited, including landowners,” says Rossi. She points out that this coordination can actually reduce the number of people stomping around on sensitive (and sometimes privately-owned) landscapes.
Monitoring Wetlands for Endangered Species
Sustaining endangered fish is always a priority for scientists and water managers in both the Delta and the Bay — so the new program is hoping to augment understanding of the importance of wetlands to these struggling species. However, collecting all the right data is tricky.
In the Delta and Suisun Marsh, a state Fish Restoration Program (DWR/CDFW) — which has been monitoring 11 mitigation and six reference sites in wetlands since 2015 — is more focused on food-web-related data than the new WRMP.
“It’s not like wetlands haven’t been monitored before in the Delta, but our management questions are different,” says Stacy Sherman, program director for Cal Fish & Wildlife and a member of the WRMP Steering Committee. “We’ve been using a whole series of methods and metrics developed via collaborative science teams for years, mainly to see if these North Delta Arc wetland restoration projects are producing food and habitat for endangered fish as intended.” Those data and standard operating procedures are publicly available at the Environmental Data Initiative, to be eventually referenced in the WRMP data portal.

Sherman would love to see the WRMP monitoring program expand to include fish food sampling for invertebrates, but acknowledges that “it’s expensive and difficult to do.” Meanwhile, she’s interested to see the WRMP data that is out of the scope of her program, such as wetland elevation change, bird use, and benefits to people.
Downstream, the WRMP will also benefit from being co-managed with other existing regional monitoring programs focused on clean water within the SF Estuary Institute. One of the most alarming changes in the Bay has been an increase in the frequency of harmful algal blooms, such as the August 2022 bloom that resulted in devastating fish kills throughout the Bay. While the WRMP does not specifically monitor for HABs, technicians collecting survey data will record qualitative observations of any fish kills or discolored water, as well as data on oxygen level spikes or crashes, information that may prove useful to parallel regional clean water monitoring programs.
All of these monitoring efforts will help the region learn more about what endangered fish need — food, habitat, and clean water — as well as which restored habitats they are using.
Scientists know endangered sturgeon and longfin smelt, for example, use restored marshes in the North and South Bay, but have yet to explore use from an estuary-wide perspective. At the end of the first two years of WRMP monitoring, Levi Lewis hopes to have enough data to do a regional comparison and begin to parse how marshes across the Bay differ in species abundance and diversity, and how those map onto environmental quality.
“If we can do that, and do that effectively, I think that the first two years of WRMP will be a great success,” says Lewis. “The Wetlands Regional Monitoring Program has been a vision, and it’s a vision that has not gone without its challenges over time and without its skeptics. It’s a huge honor to work with the folks that have maintained that vision.”
This story was produced by Estuary News Group with funding from the Delta Stewardship Council.