The ruling comes in response to a citizen complaint filed by three environmental groups.
US District judge Robert Chambers was quoted by Bloomberg as saying that the Alex Energy and Elk Run Coal have dumped high levels of contaminants into Laurel Creek and Robinson Fork streams’ aquatic ecosystems.
"In multiple ways, the chemical and the biological components of the aquatic ecosystems found in Laurel Creek and Robinson Fork have been significantly adversely affected by the defendants’ discharges," added Chambers.
The White Castle surface mine and the East of Stollings surface mine in Boone County, West Virginia are owned and operated by Elk Run, while Alex Energy owns the Robinson North surface mine and the Wildcat surface mine in Nicholas County, West Virginia.
Alpha Natural Resources spokesman Ted Pile said that the company would appeal the ruling and expects it to be reversed.
"This decision essentially strips the state of West Virginia of its legitimate role as the primary regulatory authority for state waters and substitutes in its place the federal court as the primary authority," Pile added.