The cleanup will focus on select contaminants — polychlorinated biphenyls, copper, lead and mercury — left by the Navy when the base was active. The goal is to remove contaminants that endanger animals that live in bay mud, as well as birds and humans that eat the contaminated shellfish and fish harvested from the water around the site.

Community advocates have called the agreement a “back door deal” that doesn’t fully address the radioactive contamination the Navy left in the soil at the site.

Work won’t start until 2027 after the Navy completes remedial design and planning. It will take about two years to complete the more than $30 million project; the Navy has yet to select a contractor to carry out the work or landfill to dispose of the waste.

The polluted sediment could be removed or remediated with dredging, treatment in place, capping or natural processes that eradicate the contaminants over time. The U.S. EPA and the California EPA oversee and enforce the Navy’s cleanup actions.

The 866-acre Hunters Point Naval Shipyard site was home to a shipyard from 1945 to 1974 and the Naval Radiological Defense Laboratory from 1948 to 1960. By decontaminating ships after atomic bomb tests and other activities, the Navy contaminated shipyard soil and groundwater — as well as surface water and sediment in the San Francisco Bay — with radioactive chemicals, heavy metals and petroleum fuels. The base was declared one of the nation’s most contaminated sites in 1989.

The agencies overseeing the cleanup alongside the Navy spent at least six years figuring out the best way to clean up the underwater portion of the site because it poses a risk to people and wildlife.

Cleanup of the site began in 1996.

“You don’t have to be an engineer to do the math, but that’s 28 years,” said Eileen White, executive officer of the San Francisco Bay Regional Water Quality Control Board. “I want to thank the community who’s had to wait, but the end product is going to be great.”

The project is important as storms intensify because of human-caused climate change, said Michael Montgomery, director of the EPA’s Superfund and Emergency Management Division.

“Very large storms can cause disruption,” he said. “So, in terms of super storms, the remedy would help prevent contamination from shifting.”

Bayview residents including Arieann Harrison have advocated for the complete cleanup of the site for decades. Harrison, founder and CEO of the Marie Harrison Community Foundation, said community members felt blindsided by the plan.