The EPA has dropped its requirement that a West Virginia farmer obtain a pollution-discharge permit for her chicken operation. But the farmer is still pushing ahead with her lawsuit against the agency.

Lois Alt, a Hardy County chicken farmer, is hoping her legal action will clarify whether chicken waste that rain washes into waterways can be considered processed wastewater and subject to regulation, as the EPA contends, or agricultural stormwater and therefore exempt from the Clean Water Act.

In June 2011, EPA officials visited Alt's "Eight is Enough Farm" where she grows chickens in eight houses for Colorado-based Pilgrim's Pride. The agency visited several other farms around the same time as part of an effort to show West Virginia officials how to curb pollution from farms that raise large numbers of chicken and livestock, and could be classified as concentrated animal feeding operations. All states are expected to reduce pollution loads under the Chesapeake Bay's total maximum daily load, or pollution diet, and they are tackling discharges from chicken, dairy and pork operations to help accomplish those goals.

The EPA requires that large broiler farms with more than 125,000 birds obtain permits if they discharge pollutants into waters of the United States. States have "wide latitude" to develop their own permit programs for farms smaller than the federal thresholds, said Jon Capacasa, director of the EPA Region III's water protection division. West Virginia's CAFO program had been recently established, and EPA inspectors conducted joint inspections with West Virginia environmental and agricultural officials to look for potential areas of concern on large animal farms that may be subject to federal regulation.

EPA inspectors observed evidence of manure on the ground outside Alt's poultry houses that was "exposed in a manner that it would come into contact with precipitation during rain events and generate process wastewater," according to the EPA's November 2011 Findings of Violation letter. In that letter, the inspectors required her to get a federal discharge permit or face fines as high as $37,500 a day.

But on Feb. 13, 2012, Alt's attorney sent a letter to the EPA indicating she would not be doing so because there was "no discharge." Then, in June, Alt and her attorney, David Yaussy, filed a lawsuit alleging the EPA overstepped its authority. Agricultural stormwater, they argued, was exempt from the Clean Water Act, and the EPA's attempt to re-classify it as "process wastewater" was unfair.

The court granted the American Farm Bureau Federation and the West Virginia Farm Bureau intervenor status in the case on Alt's behalf. The Potomac Riverkeeper, West Virginia Rivers Coalition, Waterkeeper Alliance, Center for Food Safety, and Food and Water Watch filed to be intervenors on behalf of the EPA in December.

Capacasa's December 2012 letter to Alt said their pursuit of the permit was "no longer warranted" because of some corrective action she'd taken since the inspection. The letter also said that, "barring a significant change of circumstances," the EPA would not issue a similar order in the future.

But Yaussy said the small changes Alt made at her farm wouldn't have necessarily reduced the amounts of manure that concerned the EPA. Alt, who already had a reputation as a conscientious farmer, began using a conveyor and hopper to clean out her house after hearing the EPA's concerns, and told the EPA she would continue to do so.

Capacasa said he could not elaborate on why the agency dropped the permitting requirement for the Alt farm because the litigation is pending.

He said his agency is focused on reducing pollution from concentrated animal feeding operations in the region's three "hot spots" — The Delmarva Peninsula; Lancaster County, PA; and the Shenandoah Valley.

"Under the Clean Water Act permitting program, states have a primary role, but we have the ability to do direct oversight and direct enforcement," Capacasa said. "And in each of the areas of focus, EPA has conducted a considerable amount of outreach to help farmers understand what qualifies as a CAFO."

But farm bureau officials said the EPA is attempting to overreach after a federal lawsuit dealt the agency a blow. In March 2011, a federal judge in the U.S. District Court of Appeals for the 5th Circuit in New Orleans ruled that the agency could only force farmers to obtain discharge permits if they actually discharged pollution. Prior to that ruling, the agency had been requiring poultry and livestock farmers to obtain the permits if their farm "proposed to discharge," or was constructed in such a way that a discharge was likely. Under that definition, most of the Delmarva Peninsula's chicken farmers would have needed permits, because of the heavily ditched soils and the high water table.

When Upper Potomac Riverkeeper Brent Walls visited the farm after the EPA action, he agreed it was clean and well-maintained. But, Walls said, the farm was constructed in such a way that trenches from the poultry house eventually led to waterways. If a large farm near a waterway like Alt's doesn't need a permit, Walls said, he doesn't know who would.

"This is the very low bar," Walls said. "If this doesn't go, then where's the bar going to reach? If they are able to get out of this, the farm bureau and all the industry out there is going to say, 'our farm doesn't qualify either.' "

But if the agency is going to go after the state's most lauded farmers, then other growers wonder who will be next, said Joan Harman, the West Virginia Farm Bureau's director of public relations. Harman also said Alt asked the inspectors to show her where she was discharging and how she could improve her operation. Capacasa's original letter to Alt did not say she was discharging, only that a discharge was possible.

Steve Butler, the West Virginia Farm Bureau's administrator, said Alt is pursuing her case for the benefit of other farmers, hoping to win a ruling that invalidates the EPA's view that pollutants that enter the water via rainfall are processed wastewater and strengthens the farmers' contention that it is agricultural stormwater and exempt from Clean Water Act regulation.

"Agriculture stormwater is not regulated in the Clean Water Act, and that has never been changed," Butler said. "Those who are doing conscientious farming, we need to let them farm, and know when it rains, they're not going to be in trouble. And those who need help, we'll help them. That will help us clean up the Bay. We will not be able to clean up a Bay by issuing a permit, and not saying, 'this is what you're doing wrong.'"

Yaussy said Alt is pursuing the case with the hope of clarity not just for other farmers, but for herself. Capacasa's second letter said they would not issue a similar order "barring a significant change," but it's not clear to him what that would be, or why the agency dropped the request in the first place. Like many farmers, Yaussy said, Alt does not wish to fall under a permit for fear of increased paperwork and possible future monitoring requirements.

"We're grateful that the EPA did that, but it's not really clear to us what that was based on, and we don't know what is going to happen in the future," Yaussy said. "We hate to look a gift horse in the mouth, but we do want to understand why they did what they did."