Experts say the agency is playing catch-up to solve a problem that began when it required power plants in the 1990s to scrub their air pollution to remove sulfur dioxide. An unintended consequence was that the pollutants captured were dumped into landfills and ponds, many unlined, where they seeped into underground aquifers or were piped into adjacent rivers, reservoirs and lakes.
"As you are pushing air rules that are definitely needed, you need to think of the water. And they didn't," said Eric Schaeffer, a former EPA enforcement official who now heads the Environmental Integrity Project, a group whose research has uncovered previously unknown sites of contamination from power plant waste pits. "Now they are running after the problem."
The federal government has in recent years issued the first-ever regulations for mercury released from power plant smokestacks, the largest source of mercury entering waterways. The EPA has also stepped up its review of mountaintop mining permits, to reduce pollution.
"Coal-related pollution remains a significant contributor to water quality pollution across the United States," said Alisha Johnson, a spokeswoman with the EPA. "The EPA's efforts have yielded significant improvements, but significant work still remains."
On the mining side, a review of federal environmental enforcement records shows that nearly three-quarters of the 1,727 coal mines listed haven't been inspected in the past five years to see if they are obeying the nation's water pollution laws. And 13 percent of the fossil-fuel fired power plants are not complying with the Clean Water Act.
Many mines don't even report their discharges of selenium, although researchers have found the chemical near mines at levels where it can cause deformities and reproductive failure in fish.
A study in the journal Science in 2010 found that 73 of 78 West Virginia streams in mountaintop mine removal areas had selenium levels higher than the official threshold for fish life. Higher levels of selenium - a natural component of coal that seeps from rock when water runs through it - often means fish don't reproduce or have deformed, even two-headed, offspring, Lemly said.
University of Maryland environmental sciences professor Margaret Palmer spent much of the weekend that Charleston was without water testing the Stillhouse Branch stream near Clay, W.Va., just below a mountaintop removal coal mine. She said her tests showed the water was too salty from the rocks from the mine.
"It's like a desert with a few water rats in it," Palmer said. "The organisms that do live in (these streams), you think of them like water rats. Only the really hearty ones survive."
Efforts by the EPA to ease the problem, by requiring mine permits to be judged by a measure of the saltiness in downstream water, have been vacated by a federal court. That decision is now under appeal.
A spokesman for the National Mining Association said the industry operates in accord with extensive and rigorous permitting guidelines.
In addition, pollution still enters the environment from coal mined decades ago.
The EPA estimates 12,000 river miles are tainted by acid mine drainage from long-shuttered coal mines. One of them is Raccoon Creek in southeastern Ohio.
"These mines have been abandoned for a hundred years," said Amy Mackey, Raccoon Creek's watershed coordinator. "There is no one to fall back on."
States take the lead on the water pollution front, but advocacy groups from at least three states in coal country - Kentucky, West Virginia and Indiana - have asked the EPA to step in, arguing that state officials aren't doing enough.