Representatives for Alpha Natural Resources, which owns Alex Energy, did not immediately return a phone messages seeking comment.
It is the policy of Consol, which owns the other two mines, not to comment on pending litigation, spokeswoman Lynn Seay said.
"CONSOL Energy strives to be a good corporate citizen in the communities where we operate, and as such, we strive to comply with all of our regulatory, contractual and other legal obligations," she added. "Once we have had a chance to review these complaints, we will respond appropriately."
Mountaintop removal is a particularly efficient but destructive form of strip mining that blasts apart mountain ridge tops to expose multiple seams of coal. The practice of flat-topping the mountains, then filling valleys and covering streams with rubble has divided communities and led to confrontations between coal miners and environmentalists.
Consol was ordered to pay a civil penalty of nearly $270,000 in a settlement reached in December with state regulators concerning violations at its Peg Fork mine in Mingo County. The groups argue the settlement doesn't specify a timeframe for the company to bring its selenium discharges into compliance. They also argue the penalty was not adequate "to disgorge Consol of its economic benefit of noncompliance."
Such lawsuits are prohibited as long as the state has "commenced and is diligently prosecuting" to require compliance. But the groups argue the state is doing so, which "leaves a realistic prospect that Consol's unlawful selenium discharges will continue," the groups allege.
They are asking the courts to require the companies to abide by pollution regulations or to pay civil penalties up to $37,500 per day for each violation.