WASHINGTON — The Biden administration on Wednesday took a major legal step toward protecting Bristol Bay in Alaska, one of the world’s most valuable sockeye salmon fisheries that also sits atop enormous copper and gold deposits long coveted by mining companies.

Citing its authority under the 1972 Clean Water Act, the Environmental Protection Agency proposed a legal determination that would ban the disposal of mining waste in the Bristol Bay watershed. It’s a move that could deal a death blow to the proposed Pebble Mine, an intensely disputed project that would have extracted the metals but also irreparably harmed the ecosystem, scientists said.

The proposal, which would create permanent protections for the waters and wildlife of Bristol Bay, about 200 miles southwest of Anchorage, will be finalized later this year.

The determination would prohibit any entity from disposing mine-related waste within 308 square miles around the site of the proposed Pebble Mine project. That’s an area about four times as large as Washington, D.C., but just a small fraction of the entire 40,000- square mile area of the Bristol Bay watershed.

“The Bristol Bay watershed is a shining example of how our nation’s waters are essential to healthy communities, vibrant ecosystems, and a thriving economy,” said Michael S. Regan, the administrator of the Environmental Protection Agency. “E.P.A. is committed to following the science, the law, and a transparent public process to determine what is needed to ensure that this irreplaceable and invaluable resource is protected for current and future generations.”

Blocking the Pebble Mine would be a promise kept for President Biden, who pledged on the campaign trail to “listen to the scientists and protect Bristol Bay.”

Extolling the region as foundational to the way of life for Alaska Natives, a prized destination for anglers and the source of half the world’s sockeye salmon, Mr. Biden said, “It is no place for a mine.”

The fight over the fate of Pebble Mine and Bristol Bay has raged for more than a decade. The plan to mine Bristol Bay was scuttled years ago under the Obama administration, then found new life under President Trump. But opposition, from Alaska Native communities, environmentalists and the fishing industry never diminished, and even Mr. Trump’s son, Donald Trump Jr., a sportsman who had fished in the region, came out against the project. The waters are thick with chum, coho, sockeye and pink salmon.

In 2020, the Army Corps of Engineers denied a permit for the project that was seen as critical for it to proceed.

The company seeking to build the mine, the Pebble Limited Partnership, appealed that decision and is also expected to challenge the legality of the Biden administration’s new plan to protect Bristol Bay.

The company wants to dig an open-pit mine more than a mile square and one-third of a mile deep where it would process tens of millions of tons of rock a year to extract metals estimated to be worth at least $300 billion. The project would include the construction of a 270-megawatt power plant and 165-mile natural-gas pipeline, as well as an 82-mile road and large dammed ponds for the tailings, some of them toxic. It would also require dredging a port at Iliamna Bay.

Both federal and state agencies found that the proposed Pebble Mine, which would be located in two watersheds that feed fish-spawning rivers, would cause permanent damage, harming the breeding grounds for salmon that are the basis for a sport fishing industry and a large commercial fishery in Bristol Bay. Salmon are also an important part of the diet of Alaska Natives who live in small villages across the region. Scientists say the mine would destroy more than 130 miles of streams, 2,800 acres of wetlands and 130 acres of open water.

Last fall, as the Environmental Protection Agency indicated that it intended to block the project, a spokesman for Pebble Mine Partnership said that doing so could have the unintended consequence of hampering the Biden administration’s goals to combat climate change, by restricting domestic extraction of a crucial mineral used in making batteries for electric vehicles and other low-carbon technologies.

“As the Biden Administration seeks lower carbon emissions for energy production, they should recognize that such change will require significantly more mineral production — notably copper,” said Mike Heatwole, the spokesman, in a statement. “The Pebble Project remains an important domestic source for the minerals necessary for the administration to reach its green energy goals.”

The Biden administration contends that there is significant economic value in conserving Bristol Bay. The E.P.A. found that the Bristol Bay commercial salmon fishery generated $2 billion in economic activity in 2019 and that the economic activity generated by the fishery created 15,000 jobs.

Agency officials said they would accept public comments on the proposal until July 5 before publishing a final legal determination.

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