CHARLESTON, W.Va. -- In another significant legal victory for the coal industry, a federal judge on Friday refused to block a Clean Water Act permit for a mountaintop removal permit in Logan County.

U.S. District Judge Robert C. Chambers ruled against an effort by the Ohio Valley Environmental Coalition to stop the Reylas Surface Mine, proposed by Highland Mining, a subsidiary of Alpha Natural Resources.

Chambers said that scientific evidence clearly shows mountaintop removal is damaging water quality and aquatic life downstream from mining operations. But the judge said a previous appeals court ruling tied his hands, forcing him to defer to the Corps of Engineers' permit approval.

In a 31-page decision, Chambers made clear he was bound by a 2009 ruling in a case involving Aracoma Coal Co., in which the 4th U.S. Circuit Court of Appeals said he overstepped his authority in throwing out four permits issued by the corps.

"This court must adhere to the guiding principles of deference under Aracoma in ruling on plaintiffs' challenges to the corps' decision, despite substantial scientific evidence contrary to that decision," Chambers wrote.

The judge defended the corps, which faced harsh criticism from citizen group lawyers, saying it was neither required nor practical for the agency to "retain experts in the myriad of issues which it confronts across the nation on a daily basis."

Instead, Chambers said, it was perfectly acceptable for the corps to rely on water quality determinations made separately by officials from the W.Va. Department of Environmental Protection, which processes water pollution discharge permits and signed off on the permit at issue.

The judge noted, however, growing concerns about mountaintop removal's effects, and the heated dispute between the U.S. Environmental Protection Agency and the DEP over how such mining should be regulated.

"Miles of West Virginia streams are being buried under valley fills covering hundreds of acres, dramatically altering the landscape and streams throughout Southern West Virginia," Chambers wrote. "The EPA and the WVDEP have been at loggerheads in evaluating these impacts and taking action to strike the balance between the state's economic interests in mining and its obligation to protect West Virginia's environment."

While the decision technically involves only one permit, the ruling also sets a standard for how other permit decisions might be made moving forward.

Ted Pile, a spokesman for Alpha, said the company was pleased with the ruling and hopes it "will bring some certainty" to the permitting process in West Virginia.

Officials from the corps could not immediately be reached for comment late Friday afternoon. A lawyer for the citizen groups declined comment.

The ruling comes just two weeks after a major decision in which a federal judge in Washington, D.C., threw out EPA water quality guidance aimed at reducing the damaging effects of mountaintop removal. The Obama administration EPA had already lost two earlier legal challenges to its tougher review of mining permits and its veto of the water pollution permit for the largest mountaintop removal mine in West Virginia history.

In mountaintop removal, coal operators use explosives to blast off entire hilltops and uncover valuable low-sulfur coal reserves. Leftover rock and dirt is shoved into nearby valleys, burying streams.

Industry officials consider the method to be highly efficient and the only way to reach some thin seams of Appalachian coal. Critics point to the fewer number of workers mountaintop removal needs, and to a growing body of science that shows forests, water and community health are threatened by mining practices.

At issue before Chambers was a Clean Water Act "dredge-and-fill" permit needed for Alpha for its 635-acre Reylas Surface Mine near Ethel in Logan County.

Alpha hopes to employ about 100 people for six years of mining, and then create a 235-acre site with paved roads and utilities that could be used for temporary housing during flooding and other emergencies. The mine, though, would bury about 2.5 miles of streams beneath a valley fill and associated runoff-control structures.

The Ohio Valley Environmental Coalition and other citizen groups argue that the mine would add to existing pollution problems in the Dingess Run watershed, and that the corps did not allow public input on the company's proposal to mitigate mining damage.

Already, Chambers had ruled against the citizen groups on several issues, including an effort to introduce as evidence peer-reviewed studies that show residents living near mountaintop removal face increased risks of serious illnesses, including cancer and birth defects. After a four-day trial in May, the judge was left to decide allegations that the corps' assessment of the mine's potential cumulative impacts was "arbitrary and capricious," a typical legal standard for overturning an agency decision.

Chambers ruled that some of the corps' key moves concerning the permit -- such as its determination that the impacted watershed was not already seriously impaired by past pollution -- were acceptable and reasonable.

The judge said he remains "extremely skeptical about the viability" of coal company plans to rebuild or replace streams buried by valley fills, but was prohibited by the 4th Circuit's previous decision from second-guessing the corps on that subject.

Chambers also said that during trial the citizen groups "presented unrefuted evidence of a correlation between mining" and electricity conductivity pollution, decreased scores on West Virginia's measure of stream health, and the loss of sensitive aquatic insects in waters downstream from valley fills.

"The testimony of plaintiffs' experts was compelling, and the efforts by the corps and [Alpha] to discredit them were in vain," the judge wrote. "The court is thoroughly convinced that large-scale surface mining is strongly correlated with elevated levels of conductivity and the loss of sensitive macro-invertebrates downstream of valley fills. This conclusion, however, is not enough to vacate the corps' decision on the Reylas permit."

Reach Ken Ward Jr. at kw...@wvgazette.com or 304-348-1702.