In the midst of the Trump administration’s dramatic policy shifts and contractions for the federal government’s natural resource agencies, the U.S. Environmental Protection Agency this month announced $82 million in grants for San Francisco Bay water quality projects—such as pollution cleanup and habitat restoration—the most the program has ever awarded at once.

“It’s incredibly encouraging to see, because this is funding that’s actually been long delayed by the administration,” says Josh Quigley, policy manager at the nonprofit Save the Bay, which has advocated for the San Francisco Bay program. Last year the grant program was held up while the Trump administration reviewed its authority. The program has been funded at around $55 million per year since it was founded in 2022, so this year’s big pot is about a year and a half’s worth of funding, according to Luisa Valiela, the longtime program manager. Grantees are required to come up with a 25 percent match, which puts the total investment in the area at around $102.5 million.

“Like we always do, we receive more applications with more need than we can give,” Valiela says. “But we’re really excited about funding these 20 projects with the available funding.”

A Biden-era Bipartisan Infrastructure Law bump to the program is history, along with its environmental-justice focus; some grants were cancelled. Yet the types of projects being funded now are similar to past years. Gone are terms like “climate change,” “climate adaptation,” or “environmental justice.” But “shoreline resilience” and “legacy contamination” projects have been funded. And a list of 11 priorities for the program is unchanged from a September 2024 snapshot, focusing on thorny ongoing environmental issues like pollution, wetland and coastal restoration, and green infrastructure.

“Everything that we do, including the way that we deploy grant funding, is focused on looking at our statutory authorities under the Clean Water Act,” says Mike Martucci, acting regional administrator for EPA’s Region 9. Looking at the funded projects, he says, “what they all share in common is we’re delivering clean water, and clean water is not a partisan issue.”

“I don’t actually see a significant change in investments,” Quigley says. “We’re seeing investments in water quality. We’re seeing investments in shoreline adaptation and habitat. We’re seeing investments, luckily, in communities that really have significant need,” like a $3 million grant to the City of Oakland to clean up PCBs from Arroyo Viejo Creek, which drains into the Bay. He noted, however, that community-led environmental justice work is no longer part of the mix.

The 17 grantees are all local or state agencies and nonprofits. Among them, the Port of Oakland and the City of San Leandro will install trash capture devices in stormwater drains. Grants to the Association of Bay Area Governments and the Metropolitan Transportation Commission will address tidal restoration along State Route 37, a North Bay highway that is slipping into the sea. The State Coastal Conservancy is tackling another piece of the South Bay Salt Ponds restoration. The Richardson Bay Regional Agency will restore eelgrass and remove marine debris off Sausalito’s shoreline. (The full list of grantees is below.)

The largest amount, nearly $15 million, is going to the nonprofit San Francisco Estuary Institute for four projects on eelgrass restoration, nutrient management and wetland restoration, reducing anglers’ exposure to polluted fish, and the Wetlands Regional Monitoring Program. 

Sami Araya leans out from the R/V Lonsme to collect some marsh treasures for the Wetlands Regional Monitoring Program, which the EPA is helping fund. “Our goal is to be able to tell the story about how the estuary is changing over time,” Aviva Rossi, lead WRMP scientist with the San Francisco Estuary Institute, told Bay Nature last year. Tanvi Dutta Gupta / Bay Nature

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The San Francisco program has been characterized by “a long history of success,” Martucci says. “It really is something that has been an awesome partnership between the federal government, local governments, state government, our not-for-profit partners, and others.” 

“When you think about the challenges of an urban sea, and just so many people living so close to a complex ecosystem, and the environmental challenges that that creates—but at the same time, a lot of opportunity, with the partnerships—I think that that is why this administration and I feel so strongly about continuing our investments in these places,” Martucci says. “The investments of our time and our folks are just reaped back in dividends.”

Meanwhile, the Trump administration is proposing for fiscal year 2027, as it did last year, to eliminate the San Francisco Bay program outright. Puget Sound is the only other geographic program that was targeted with a proposed partial cut. The rationale, the budget proposal says, is “to recognize that substantial progress has been made to clean up the Bay and to provide the opportunity for more state and local support.” EPA Region 9 did not prepare that proposal, Martucci says.

“We look forward to Congress’s feedback on this,” Martucci says. “At the end of the day, the agency will deliver on the budget that we’re given by Congress.”

What’s being funded

Here’s the full list of grantees, from the EPA announcement:

• Association of Bay Area Governments ($5.6 million): This funding will support habitat restoration at Strip Marsh East along Highway 37 in San Pablo Bay by reusing sediment produced from excavating new tidal channels and lowering berms. The project will also deliver a report on how sediment moves through the Bay-Delta estuary to inform long-term plans to restore 100,000 acres of tidal wetlands in the region.

• Bay Area Clean Water Agencies ($7 million): This funding will support five pilot projects aimed at reducing nutrient inputs to San Francisco Bay. The projects will test biological nutrient removal technologies at wastewater treatment plants, advance nature-based approaches for nutrient management, and develop a regional nutrient trading program.
• City of Oakland ($3 million): This funding will support the cleanup of legacy polychlorinated biphenyls (PCB)-contaminated soil from Arroyo Viejo Creek. Harmful PCBs accumulate in the environment and fish, which can lead to impacts on human health when those fish are consumed. The project will remove 2,500 cubic feet of PCB contaminated sediment from the creek bed, preventing it from entering the Bay.
• City of San Jose ($3.16 million): This funding will support the City of San Jose’s green stormwater infrastructure implementation plan. A new approach will be added under the City’s stormwater permit requirements to allow new development projects to pay into an “operations and maintenance” fund for existing green stormwater infrastructure.
• City of San Leandro ($2.49 million): This funding will help reduce trash and pollutants entering the San Leandro Bay by installing two large trash capture devices in stormwater drains in San Leandro Creek.
• City of San Pablo ($1.26 million): This funding will support the construction and monitoring of green stormwater infrastructure facilities designed to capture and treat large volumes of stormwater runoff.
• East Bay Regional Park District ($5 million): This funding will support restoration of tidal marsh habitat at Hayward Marsh. The project will include the installation of approximately 1,200 feet of living shoreline and enhancements of wetlands and marsh habitat to improve ecological complexity and water quality.
• Marin Audubon Society ($5 million): This funding will help restore 4 acres of tidal marsh along the Marin County shoreline and protect existing marsh through construction of a 2-acre cobble beach. Beaches are a nature-based solution that can protect inland property from erosion and sea level rise.
• Metropolitan Transportation Commission ($9.57 million): This funding will improve tidal circulation in Tolay Creek and nearby wetlands by expanding the width under the State Route 37 bridge. The project will also reuse excavated sediment to reinforce flood protection levees at nearby facilities.
• Port of Oakland ($5 million): The funding will support the Port of Oakland’s installation of four large trash capture devices which will collect stormwater from 427 acres of port property. The devices will reduce more than 4,700 gallons of trash from entering the San Francisco Bay.
• Richardson Bay Regional Agency ($3.05 million): This funding will support the removal of legacy marine debris from Richardson Bay to improve subtidal habitat and advance eelgrass restoration efforts. The project will map, remove, and characterize 700 to 900 tons of debris and help restore six acres of eelgrass habitat.
• San Francisco Estuary Institute: The four following grants are awarded to the San Francisco Estuary Institute for separate projects:
  • Advancing Eelgrass Restoration ($1.83 million): This funding will support the development of a regional dataset for subtidal eelgrass habitat in San Francisco Bay. The project will evaluate regionwide eelgrass monitoring options, identify cost-effective strategies, and develop standard operating procedures to support restoration goals.
  • Nutrient Management and Wetland Restoration ($4.09 million): This funding will ensure continued nutrient monitoring in San Francisco Bay and evaluate the results of nutrient-focused wetland restoration projects and wastewater treatment plant upgrades. The project will track harmful algal blooms, collect data on changes in water quality, and inform future nutrient trading programs.
  • Protecting Bay Fishers: Management of PFAS, PCBs, and Other Contaminants ($3.18 million): This funding will support fish monitoring, consumption surveys, and efforts to reduce exposure to contaminants in San Francisco Bay. The project will help update Bay Area fish consumption advisories, inform cleanup plans for mercury, PCBs, and PFAS, and improve public health for Bay fishers and their families.
  • Wetlands Regional Monitoring Program ($5.86 million): This funding will support the Wetlands Regional Monitoring Program by expanding water quality and fish monitoring efforts. The project will provide baseline data, standardize monitoring requirements, and inform decisions on future regional restoration investments.

• San Mateo City/County Association of Governments ($3.8 million): This funding will support targeted monitoring of PCBs, implementation and evaluation of efforts to control PCB sources, and public outreach in San Mateo County. Removal of PCBs from Bay Area watersheds is required under the stormwater permit to protect Bay fish from bioaccumulation.
• San Francisco Public Utilities Commission ($5 million): This funding will support construction of green stormwater infrastructure throughout the Outer Mission neighborhood in San Francisco, including planted sidewalk filtration systems, rain gardens, and an underground system that helps water soak into the ground.
• Solano Land Trust ($3.99 million): This funding will help restore tidal flow to 80 acres of marsh at Rush Ranch as part of the Goat Island Restoration Project. The project will expand high-quality habitat, remove invasive plants, improve public access, and support long-term monitoring of the marsh and special-status species.
• State Coastal Conservancy ($3 million): This funding will advance the South Bay Salt Pond Restoration Project by restoring 275 acres of tidal marsh habitat in Pond A1. The project will reconnect Pond A1 to the San Francisco Bay, add shoreline erosion protection, and plant native vegetation to enhance habitat benefits.
• Trout Unlimited ($1.29 million): This funding will support the planning and permitting needed to remove a fish passage barrier in the Petaluma River watershed. By removing a failed culvert, upper watershed habitat for steelhead and Chinook salmon will be reconnected in Adobe Creek and Petaluma Marsh.