In June 2009 the U.S. Environmental Protection Agency had established a new process for issuing clean water permits in an effort to protect mining communities from polluted water.
Thursday's ruling is related to Clean Water Act "404 permits" necessary for valley fills, the industry practice of blasting excess rock from mountaintop mining sites and discarding the rock and dirt into nearby valleys and streams.
But the EPA's new quality guidance aimed at reducing pollution from the Appalachian region's coal mining operations still remain. Legal arguments on that issue, scheduled to be heard this month, have been delayed until next June.
The EPA said the ruling is a procedural issue and would not affect its authority under the Clean Water Act.
The EPA "wants to reassure families living in Appalachia that today's District Court ruling was a procedural decision that does not affect our Clean Water Act authority to protect them from public health and environmental impacts caused by poor coal mining practices," the agency said in a statement.
The National Mining Association said it was "very gratified" by the decision "to set aside EPA's unlawful process for evaluating scores of coal permits throughout Appalachia and the agency's illegitimate criteria for doing so."
The ruling is expected to remove restrictions on more than 70 mining permits for projects in Appalachia.
"With this decision, coal communities can get back to the business of producing affordable energy for Americans and put more Americans back to work," said Hal Quinn, president of NMA, an industry group that includes large miners Arch Coal Inc., Alpha Natural Resources Inc. and Peabody Energy Corp.
Environmental groups maintain that mountaintop coal mining destroys the environment. A poll released in August by CNN indicated that 57 percent of Americans nationwide oppose the practice.
"While the coal industry may have succeeded in part of one lawsuit against government agencies, we will continue to support the EPA in their role protecting U.S. families, waters and local communities, and ensure that those protections become stronger," said Ed Hopkins, director of the Sierra Club's Environmental Quality Program.
"We will continue working to protect mountains and streams, even as the coal industry tries to continue destroying them."