“This unlawful and destructive rule is nothing but a thinly veiled attempt to destroy our nation’s underground coal mines and put our nation’s coal miners out of work,” Robert E. Murray, the company’s chief executive, said in comments released ahead of Thursday’s vote.

A report released by the Congressional Research Service last month laid out the environmental and health benefits of the rule. Stream restoration requirements would reduce human exposure to contaminants in the drinking water, and the probability of adverse health effects, the report said. The replanting of trees also required by the rule would increase carbon storage and reduce emissions, aiding in the fight against climate change, the report said.

The report also outlined the costs to industry: $52 million in annual compliance costs for the coal industry as a whole, of which roughly half was expected to be borne by mining operations in Appalachia. The rule could endanger up to 590 coal mining jobs in the region, the report estimated, though the losses would be partly offset by engineers and biologists that companies would need to hire to comply with its terms.

Even without the rule, coal industry employment would shrink by more than 15,000 workers, from a total of 90,000 in 2012, the report noted.

Still, on the campaign trail, Mr. Trump had pointed to coal mining’s decline as a symptom of overzealous environmental regulation and the neglect of working-class Americans by coastal elites. He vowed that, as president, he would “put our miners back to work” — a promise that resonated with voters in battleground states, including those in Appalachia.

But the American market for coal is shrinking, with or without new rules and regulations. Utility companies have drastically reduced their reliance on coal. Nationally, about 300 coal-fired power plants have closed since 2008, according to the National Mining Association, a trade group. Many of those plants are not coming back, whatever the policy out of Washington, making it imperative that Appalachia diversify its economy, industry analysts say.