A worker with the Pebble Mine project test drills in the Bristol Bay region of Alaska. An EPA report indicates a large-scale copper and gold mine in Alaska's Bristol Bay region could have devastating effects on the world's largest sockeye salmon fishery and adversely affect Alaska Natives, whose culture is built around salmon. (Al Grillo/Associated Press)

A large-scale mining operation in Alaska’s Bristol Bay would destroy a significant portion of the watershed, a pristine fishery that supports nearly half the world’s sockeye salmon and dozens of Native villages that have relied on fishing for thousands of years, according to a report released Wednesday by the Obama administration.

The long-awaited final assessment on potential impacts of mining in the western Alaska region, compiled over three years by the Environmental Protection Agency at the request of area tribes, dealt a serious blow to a Canadian company’s ambitions to dig one of the world’s largest pit mines to extract resources from the mineral-rich land.

The company, Northern Dynasty Mining, has yet to file a permit for its Pebble Mine, but the EPA estimated that up to 94 miles “of salmon-supporting streams and 1,300 to 5,350 acres of wetlands, ponds, and lakes” would be erased by the footprint of a mining pit, depending on its size.

Based on the recent records of similar mines in the United States, the EPA projected that polluted water from the site could enter streams from dredged solid waste and wastewater runoff. “Under routine operations, EPA estimates adverse direct and indirect effects on fish in 13 to 51 miles of streams,” the agency said in a statement released in combination with the report.

Northern Dynasty and its Republican supporters criticized the report as biased, premature and bad for business. Environmental groups and Democrats hailed the assessment as a first step to protecting fish, wildlife and Alaska Natives whose way of life rely on them.

“Publication of the final watershed assessment is really the final chapter in a very sad story,” said Ron Thiessen, Northern Dynasty’s president and chief executive, who hadn’t read the document. “We believe EPA set out to do a flawed analysis of the Pebble Project, and they certainly succeeded with both their first and second drafts” of the Bristol Bay watershed assessment. “We have every expectation that the final report released today is more of the same.”

The EPA began the assessment in 2010, when tribes asked the agency to intervene after Northern Dynasty expressed interest in a major dig for copper and gold worth an estimated $500 billion.

EPA officials said granting such a request is unusual, but scientists thought a peer­reviewed study was crucial, given Bristol Bay’s historical importance to the tribes, which have fished there for thousands of years, and its distinction as one of the world’s last great, undisturbed salmon fisheries.

Thiessen noted that the assessment does not include recommendations or regulations that might affect the future development of the Pebble Project. He said Northern Dynasty would submit a proposal that can be reviewed by federal and state officials in the coming months.

“We have every expectation that the Environmental Impact Statement process . . . to be administered by the U.S. Army Corps of Engineers will ultimately provide a much more rigorous, fair and transparent review of the science surrounding this important project,” he said.

A coalition of opponents made up of Alaska Native leaders, commercial fishermen, jewelers and environmental groups had a different view. They called on the EPA to end any chance that the project can move forward.

“It’s time for the EPA to take immediate steps to protect the fishery, the Alaska Native communities who rely on it as their primary source of food and the 14,000 jobs that depend on it,” said Luki Akelkok, a sport-fishing lodge owner who is chairman of Nunamta Aulukestai, an association of 10 Bristol Bay Native tribes and Native village corporations.

“EPA’s assessment is objective, clear and grounded in sound science,” said Taryn Kiekow, senior policy analyst with the Natural Resources Defense Council. “Now . . . it is time for the agency to take regulatory action to stop the Pebble Mine.”

Dennis McLerran, administrator for the regional EPA office that oversees the watershed, said the agency is unwilling to take that step.

“We have not yet made any decisions with respect to regulatory actions,” he said in a conference call with reporters.

Still, in its analysis, based on documents submitted to the Securities and Exchange Commission by Northern Dynasty, the EPA painted a picture of potential devastation.

An 86-mile transportation corridor with the site would cross 54 streams and rivers where about 35 million adult salmon return from the ocean to spawn and young salmon migrate to the ocean to swim.

If a storage dam were to fail, it “would have a catastrophic impact on fish for decades,” said Jeff Frithsen, a senior scientist at the EPA.