A federal judge March 23 ruled that the Environmental Protection Agency (EPA) overstepped its authority when it revoked a permit for Arch Coal Inc. to proceed with its controversial Spruce No. 1 mining operation in the Appalachian mountains.

In 2007, Arch Coal obtained a “dredge and fill” permit from the U.S. Army Corps of Engineers allowing it to move forward with the Spruce No. 1 mine in rural Logan County, West Virginia. But in January 2011, EPA revoked the permit, arguing that the project would do significant harm to streams and watershed areas near the mine. The Spruce Mine had been the subject of one of the most comprehensive environmental impact statements (EIS) ever undertaken for a coal mine in the U.S.

At issue was whether EPA had the authority under Section 404 of the Clean Water Act to revoke a valid existing permit issued by another federal agency when the terms of the permit had not been abridged. In the 12 previous cases where EPA had revoked permits, it did so arguing that the company was operating outside the confines of the permitted activity. That was not the case at the Spruce No. 1 mine.

U.S. District Judge Amy Berman Jackson struck down EPA’s ruling and said the permit issued by the Corps “remains valid and in full force.” “Based upon a consideration of the provision in question, the language and structure of the entire statutory scheme, and the legislative history, the court concludes that the statute does not give EPA the power to render a permit invalid once it has been issued by the Corps,” Judge Jackson wrote.

“It’s bad enough that EPA’s crusade against Appalachian coal is harmful to coal communities and the economy of the region, but now we know it is also unlawful,” Luke Popovich, a spokesman for the National Mining Association (NMA), told the Wall Street Journal (March 24). Arch Coal said the project would create 250 jobs and represented a $250 million investment by the company.

Judge Jackson’s ruling represents a setback for the Obama administration, which has argued that the Clean Water Act gives EPA wide latitude to veto permits issued by the Corps.

“The current permitting process is already a protracted and complicated affair,” NMA CEO Hal Quinn said in a statement. “If we are to encourage investments, grow our economy and create jobs, companies need the certitude their success in obtaining permits will not be later robbed by the whims of EPA.”

Judge Jackson’s ruling was the second Clean Water Act-related defeat EPA had suffered in 48 hours. On March 21st, the U.S. Supreme Court – in a unanimous 9-0 decision – ruled that EPA must allow an Idaho couple the right of judicial review to challenge the agency’s order to cease building a home on their property. EPA claimed that a bone-dry lot owned by Mike and Chantell Sackett was a wetland and ordered the couple to cease clearing their property and return the land to its original state or face up to $75,000 in fines per day. As a result of the Supreme Court’s ruling, the Sacketts will now get their day in court.

While the two cases are different, they both revolve around the same principle. EPA is not above the law. “This is a huge victory for West Virginia and our coal miners,” Gov. Earl Ray Tomblin (D) told the Washington Post (March 25). Tomblin urged EPA Administrator Lisa Jackson “to admit that they have gone too far.”

“Issue our permits so that we can put our people back to work and provide the resources that will power America,” the governor added. In a statement, the West Virginia Coal Association was even blunter. It applauded the court “for taking EPA to task for overstepping its authority in order to wage a regulatory war on the West Virginia coal industry.”

But perhaps no one was more scathing of EPA than Judge Jackson, who wrote in her decision: “This is a stunning power for any agency to arrogate to itself when there is absolutely no mention of it in the statute.”