(Debbie Hill/DEBBIE HILL)

FOR DECADES, coal companies have been removing mountain peaks to haul away coal lying just underneath. More recently, scientists and regulators have been developing a clearer understanding of the environmental consequences. They aren’t pretty.

In the 1990s, coal miners began using large equipment to strip away mountaintops in states such as West Virginia. The technique made it economical for them to extract more coal from troublesome seams in the rock, which might be too small for traditional mining or lodged in unstable formations. Environmentalists were appalled, but the practice spread and now accounts for more than 40 percent of West Virginia coal production.

Burning coal has a host of drawbacks: It produces both planet-warming carbon dioxide and deadly conventional air pollutants. Removing layers of mountaintop in the extraction process aggravates the damage. The displaced earth must go somewhere, typically into adjoining valleys, affecting the streams that run through them. The dust that’s blown into the air on mountaintop removal sites, meanwhile, is suspected to be unhealthy for mine workers and nearby communities.

Scientists have recently produced evidence backing up both concerns. Over the summer, a U.S. Geological Survey study compared streams near moutaintop removal operations to streams farther away. In what should be “a global hotspot for fish biodiversity,” according to Nathaniel Hitt, one of the authors, the researchers found decimated fish populations, with untold consequences for downstream river systems. The scientists noted changes in stream chemistry: Salts from the disturbed earth appear to have dissolved in the water, which may well have disrupted the food chain.

Last week, the Charleston Gazette reported on a new study finding that dust from mountaintop removal mining appears to contribute to greater risk of lung cancer. West Virginia University researchers took dust samples from several towns near mountaintop removal sites and tested them on lung cells, which changed for the worse. The findings fit into a larger, hazardous picture: People living near these sites experience higher rates of cancer and birth defects.

With these sorts of problems in mind, the Environmental Protection Agency is taking a more skeptical look at mountaintop removal mining permits. The Clean Water Act gives the government wide authority over industrial operations that change rivers and streams. The EPA has already used it to revoke a permit from a controversial proposed mountaintop removal mine in Logan County, W.Va. The agency has also instructed its branch offices to be more careful about mountaintop removal projects that could change nearby water chemistry.

The coal industry and its allies are howling. Skeptics of mountaintop removal, one industry pamphlet insisted, “promote an anti-coal, anti-business agenda that uses environmental issues as a mere pawn to redistribute wealth, grab power, and put forth liberal, social ideology.” The GOP-controlled House passed a bill that would strip the EPA of some of its permitting power. But just this month the Obama administration once again prevailed in court, beating back another industry challenge.

The emerging scientific evidence should cut through the rhetoric. The EPA is right to move more firmly to protect health and environment.