"It's an affirmation of what we thought the rule was," said administrator Stephen Butler, "and it shows the EPA was overstepping its bounds."
When Congress passed the Clean Water Act, it acknowledged that storm water runoff was different from a fixed source of pollution and should not be subject to permitting, Butler said. Farmers, who work long hours to keep their operations going, were less concerned about the cost of the permits, he added, than the recordkeeping they'd have to do afterward.
Alt, who sued the EPA in June 2012, didn't immediately respond to a request for comment, relayed through her attorney.
The EPA's actions were aimed at cleaning up the Chesapeake Bay watershed, which encompasses parts of Delaware, Maryland, New York, Pennsylvania, Virginia and West Virginia, and all of the District of Columbia.
The EPA said it has long held the view that it can require a permit for manure and litter discharged from poultry houses through ventilation fans if it threatens waterways.
Siding with the EPA were environmental and consumer groups including Earthjustice, Food & Water Watch, Potomac Riverkeeper, Waterkeeper Alliance and the West Virginia Rivers Coalition. The organizations said in a written statement that they were disappointed in the court's ruling.
"The court's decision, if it stands, could have devastating impacts on the health of our rivers, streams and lakes and our communities. Moving forward, we will be considering all of our legal options," the groups said.
The groups have long argued that neither Alt's farm "nor the other tens of thousands of commercial farms like it across the country" should be exempt from federal water-protection laws.