The U.S. Environmental Protection Agency moved Friday to veto a water quality permit for West Virginia’s largest surface mine, saying the operation would cause irreversible damage to the environment.

Regional Administrator Shawn Garvin said talks with Mingo Logan Coal Corp. failed to produce an agreement to reduce potential harm at the Spruce No. 1 mine. The agency said the mining plan, which includes mountaintop removal and valley fills, would cover 2,278 acres and would bury 7 miles of headwater streams and degrade water quality.

The U.S. Army Corps of Engineers issued the permit in 2007. But EPA said it wanted to exercise its authority under the federal Clean Water Act to review the permit further.

EPA’s proposal was issued Friday, the deadline set by a federal judge for the agency to make a decision.

“This recommendation is consistent with our broader Clean Water Act efforts in Central Appalachia. EPA has a duty under the law to protect water quality and safeguard the people who rely on these waters for drinking, fishing and swimming,” Garvin said in a prepared statement.

The permit is the subject of a federal lawsuit challenging the corps’ authority to issue clean water permits for large mountaintop removal mines. U.S. District Judge Chuck Chambers has allowed mining to occur at the Logan County mine until the case is resolved.

The Ohio Valley Environmental Coalition is a plaintiff in the lawsuit. Co-director Dianne Bady said she was pleased by EPA’s decision.

“We are so glad to see the Obama administration based its decision on sound science,” she said.

Several members of West Virginia’s congressional delegation said they were upset by the decision.

Mingo Logan is a subsidiary of St. Louis-based Arch Coal. The company said it was disappointed by EPA’s action and was assessing its legal options.

“The Spruce permit is the most scrutinized and fully considered permit in West Virginia’s history,” the company said in statement. “The 13-year permitting process included the preparation of a full environmental impact statement, the only permit in the eastern coalfields to ever undergo such review.”

Arch Coal said it would ask Chambers to rule on the company’s request for summary judgment in the lawsuit. The Department of Justice asked Chambers on Friday to delay any decisions until EPA issues a final decision following a 60-day public comment period.

It’s the first time since 1972 that EPA has used its authority to veto a permitted project. In nearly four decades, the agency has used its authority only 12 times before a permit was issued.

Garvin said EPA determined that rock, dirt and other mining wastes from Spruce No. 1 would affect water quality, fish and wildlife in the Coal River watershed. The watershed is already one of the state’s more heavily mined areas.

The mine would release high levels of total dissolved solids and selenium, which in high concentrations can create birth defects in fish and other aquatic life.

Also, the plan to replace ecological resources lost during mining was inadequate, EPA said.

The federal agency has focused on coal mining in Central Appalachia since President Barack Obama took office. The agency has concentrated on mines where mountaintop removal mining is used to expose multiple coal seams. Studies have shown the mining practice has buried hundreds of miles of streams under valley fills that were permitted under the dredge and fill section of the Clean Water Act.

Last fall, EPA said it had identified 79 permits in West Virginia, Virginia, Kentucky and Tennessee where the mining practice is used. In September, EPA said it wanted to review the Spruce No. 1 permit.

Garvin said EPA will hold a 60-day comment period on its recommendation before it makes a final decision. The agency also plans to hold a public hearing in the state.