The Environmental Protection Agency set a potentially unprecedented process in motion when it began work on Feb. 28 to preemptively block Pebble mine as an effort to protect Bristol Bay fisheries.

EPA Administrator Gina McCarthy said in a formal statement the agency was initiating action to invoke its authority to veto the proposed Iliamna-area copper-gold mine under the seldom-used Section 404(c) of the Clean Water Act.

The regional U.S. Army Corps of Engineers handles Section 404 permit applications for all projects, public or private, that could impact wetlands.

Subsection 404(c) of the Clean Water Act gives the EPA the authority to veto Section 404 applications and the agency has issued 13 final veto determinations nationwide since the act became law in 1972. All of the prior veto actions came after a Section 404 permit application had been submitted, meaning Pebble would be the first case in which use of the veto power occurred without a permit application.

The entire process usually takes at least a year.

“Extensive scientific study has given us ample reason to believe that the Pebble mine would likely have significant and irreversible impacts on the Bristol Bay watershed and its abundant salmon fisheries,” McCarthy said in an EPA release.

If fully developed, the Pebble deposits could become one of the largest surface copper-gold mines in the world.

EPA’s most recent action comes after the agency issued its final watershed risk assessment of Bristol Bay in January that found large-scale mining could have “potentially destructive impacts to salmon and other fish” in the region.

Bristol Bay is home to the world’s largest commercial sockeye fishery; the 2013 ex-vessel value for all commercial salmon harvested in Bristol Bay was $140.5 million, according to the Alaska Department of Fish and Game.

The move drew immediate praise from fishing groups — sport and commercial — as a conservation-minded approach to development, as well as criticism from some political leaders.

In statements from their offices, Rep. Don Young and Sen. Lisa Murkowski both spoke out against EPA’s intent to begin blocking the mine prior to a mine plan or environmental permits being submitted.

“This expansive, jurisdictional power-grab proposed by the EPA severely jeopardizes not only Alaska’s sovereignty, but the rights of states and all private property owners nationwide,” Young said. “Today’s (Feb. 28) announcement for review under Section 404(c) of the Clean Water Act shows an agency corrupted by politics — one with no regard for the state or federal permitting processes found in the statute.”

State Attorney General Michael Geraghty sent a letter to McCarthy and EPA Regional Administrator Dennis McLerran Feb. 28 asking agency leaders to suspend the 15-day period that the state, applicant and the Corps of Engineers have to respond to the action until after permits are submitted by Pebble.

Geraghty wrote that the January watershed assessment is more than 1,000 pages long and that the state has not had a chance to fully vet it, thus making an appropriate response to the Section 404(c) action difficult.

All Pebble Limited Partnership claims are on state land, which requires state involvement in the process.

Pebble CEO Tom Collier said in a release that the group is confident in its project and will continue to work with the state and the EPA, while calling the move a step that has turned the federal permitting process “on its head.”

“The steps taken by the EPA to date have gone well outside its normal practice, have been biased throughout and have been unduly influenced by environmental advocacy organizations,” Collier said.

EPA’s announcement is the latest blow to Pebble. In September, London-based Anglo American Plc, a 50 percent owner in the Pebble Partnership, announced it would pull out of the project after it had invested more than $540 million in exploration and planning.

Remaining owner Northern Dynasty Minerals Ltd. CEO Ron Thiessen has said the company would continue to pursue other partners in Pebble.

Political leaders have asked for a yet-to-be released formal mine plan from Pebble so the decision process on the proposal can begin.

The United Tribes of Bristol Bay issued a statement saying the EPA action is “the first step toward fulfilling (the agency’s) trust responsibility to Bristol Bay’s tribes and the subsistence way of life.”

Sen. Mark Begich took a stand against Pebble shortly after the January watershed assessment was released. When asked by the Journal of Commerce whether he thought the project should be allowed to enter the permitting process, he responded with a formal statement from his office: “Pebble Limited Partnership has had years to present a final mine plan and file for permits. Even after prodding by my colleague, Sen. Lisa Murkowski, this fall, they failed to do that. Right now, the project can still apply for all of its state and federal permits.

“As I understand it, once the 404c process is underway, the company can apply for but not receive a wetlands fill permit until the process reaches an end. I made my decision, after reviewing the science and hearing from Alaskans, that this is the wrong mine in the wrong place. Residents of Bristol Bay need certainty about how to plan their future and deserve not to have this issue hanging over them forever.”

Murkowski and Young sent a letter to EPA Inspector General Arthur Elkins Jr. Feb. 12 asking him to follow up on a request by the Pebble Partnership to investigate the origination and content of the Bristol Bay Watershed Assessment, or BBWA.

“We believe the BBWA sets a terrible precedent for future development not just in our home state but throughout the nation. We therefore ask you to look into the allegations that have been raised about the BBWA, and to determine whether it is in fact impartial, based on sound science, and compliant with all relevant federal and EPA quality standards,” the letter states.

Bristol Bay Native Corp. President and CEO Jason Metrokin said a vast majority of the company’s shareholders and area residents oppose the mine.

“Bristol Bay Native Corp. appreciates that EPA will identify appropriate options to protect Bristol Bay from the risks Pebble poses,” Metrokin said in a formal statement. “While BBNC supports responsible development, including mining, the science has shown that the proposed Pebble mine presents unacceptable risks to Bristol Bay salmon, people and existing economies.”