Lois Alt is a trained electrician, a proud West Virginian, a loving mother and a doting grandmother.

She also happens to be the little lady who started the next big chicken war.

Alt, 61, is suing the EPA after inspectors visiting her Old Fields farm in 2011, found her in violation of the Clean Water Act, and ordered her to obtain a discharge permit for a Concentrated Animal Feeding Operation, or CAFO. CAFOs are regulated as a point source of pollution, much like a sewage treatment plant is.

Though the EPA later re-inspected her farm and rescinded the order, Alt is continuing to pursue the case. She wants a judge to clarify whether the EPA has jurisdiction over operations like hers — family farms with several chicken houses that many environmentalists and lawmakers would like to regulate as point sources.

“My name may be on this case, but we’re doing this for all farmers, everywhere,” Alt said. “If farmers can’t stick together, then there’s not much coming to us, is there?”

The crux of Alt’s complaint is in the way the EPA defines runoff that comes from the chicken houses. The EPA’s Findings of Violation notice said that dust from the chicken houses’ exhaust fans settles on the ground and can contain manure, dander, feathers and other pollutants. Inspectors found trace amounts of manure that could come into contact with rain and generate “process wastewater that is carried into the nearby man-made ditches,” according to the order. The runoff could then enter Mudlick Run, a stream on the Alt’s property that eventually connects with the south branch of the Potomac River.

The EPA, in its compliance guide for CAFOs, defines process wastewater as “water used directly or indirectly in the operation of an animal feeding operation for any or all of the following: spillage or overflow from animal or poultry watering systems; washing, cleaning or flushing pens, barns, manure pits and other facilities; direct contact swimming, washing or spray cooling of animals; and dust control.” It also includes any water that comes into contact with raw materials, such as feed, litter, manure and bedding. The EPA’s definition does not say anything about rainwater.

Alt’s attorney, David Yaussy, argues that any water related to precipitation and running off her farm is not “process wastewater,” but plain old agricultural stormwater, which he says the agency does not have the authority to regulate under the Clean Water Act.

He is asking a federal judge to declare that any water coming into contact with dust from the poultry fans or trace amounts of manure on the ground is agricultural stormwater and exempt from the Clean Water Act, and that the agency’s requirement that Alt obtain a permit to operate as a CAFO is “arbitrary, capricious, not in accordance with law, and in excess of EPA’s jurisdiction and authority.”

Both the West Virginia Farm Bureau, which is financing Alt’s defense, and the American Farm Bureau Federation have been granted intervener status in the case.

On the other side is a coalition of environmental groups, including the Potomac Riverkeeper, Food and Water Watch, and Earthjustice. They are asking the court to uphold the EPA’s authority under the Clean Water Act to regulate waste from poultry farms, especially large ones like Alt’s. Her farm, Eight is Enough, has eight chicken houses. She raises about 200,000 birds a year. Many poultry farms on Delmarva are smaller, with just two or three houses.

“If Lois Alt’s farm isn’t a CAFO, then none of them are, and we might as well give up,” said Scott Edwards, an attorney who co-directs the Justice Project for Food and Water Watch. “This industry is polluting these waterways at an astonishingly alarming rate. They should all be getting permits.”

It is not about the way Alt runs her chicken farm, said the Potomac Riverkeeper’s Robin Broder. It’s about all poultry farms, bad actors and good ones, being held accountable under an enforceable permit that regulates what, when and how much they can discharge into waterways.

Broder called the case “another attempt to weaken the EPA’s authority to regulate pollution from agricultural sources.” She said the case was “an important opportunity to support the EPA.”

The EPA has struggled over how to regulate farms for decades, and has suffered setbacks in Congress and the courts. Recently, National Pork Producers prevailed in a Louisiana court after the EPA tried to regulate farms that could discharge into waters of the state. The court ruled that the discharge had to be real, not theoretical. The decision is only binding in the 5th Circuit, which covers Louisiana, Mississippi and Texas. Court challenges and the different politics in states with agricultural industries have led to inconsistent rules.

If the judge in the Alt case decides that her farm’s discharges are stormwater and therefore not subject to regulation, that could mean that hundreds of other large animal operations do not need permits. If the judge decides that Alt’s discharge is regulated, it would bolster the EPA’s attempts to regulate discharges.

EPA officials did not respond to e-mails seeking comment for this story. But in an interview several months ago, Jon Capacasa, who directs the water protection division at the EPA’s Region 3 headquarters in Philadelphia, said tightening CAFO regulations was a focus of President Obama’s 2009 Chesapeake Bay Executive Order, which charged the agency with accelerating the Chesapeake’s cleanup.

Capacasa said the agency turned its attention to the three areas in the watershed with the largest number of animal feeding operations: Lancaster County, PA; the Delmarva Peninsula; and the Shenandoah Valley. The agency considered Alt’s farm to be within the Shenandoah area; Hardy County, WV, is home to many chicken growers as well as a major plant for Pilgrim’s Pride.

Capacasa said the EPA has two roles: Enforcing the national CAFO rule, which covers chicken farms with more than 125,000 birds and with a discharge into waters of the United States; and helping the states comply with their pollution-reduction commitments under the total maximum daily load.

“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. “In each area of focus, EPA has conducted a fair amount of outreach to determine what qualifies as a CAFO.”

West Virginia was still defining its CAFO program, and the EPA wanted to educate state inspectors about what constituted an animal feeding operation. It used flyovers and maps to identify large poultry farms and chose four to inspect. Lois Alt’s was one of them.

Alt, a longtime electrician for the construction industry, saw the poultry business as a respite from her long commute to Virginia. She took pride in maintaining her eight houses, and often invites her grandchildren over to see the chicks. She and her husband, Tony, invested their life savings in the farm, which they bought from a neighbor who found eight houses were too much for him to maintain.

Alt said they learned a lot about maintenance along the way, as well as the connection with the Chesapeake Bay. She said they invested about $4,000 of their own money on a concrete pad to avoid the inadvertent spreading of manure. On a recent visit, even after a major rain, the farm looked dry and clean. The chicken houses, which often smell like ammonia on other farms, carried nothing more than the faint aroma of sawdust.

Alt felt confident in her maintenance practices, but she still worried about the inspection. She called Pilgrim’s Pride, the Colorado-based company she’d raised chickens for since she and her husband, Tony, bought the 24-acre farm in 2001. They told her they had no concerns. Lois Alt was one of their best growers, earning an environmental award nearly every year for her stewardship. Some local hands even refused to work for the Alts because they were so particular, requiring extra sawdust bedding for their chickens and cleaning out the houses twice a year instead of once.

The EPA’s inspectors arrived on the farm in June 2011. They showed Alt aerial photographs of her farm. From the photographs, it appears that the eight chicken houses are next to the stream, with just a small tree buffer separating them. But in reality, a small hill runs up to an embankment, and Mudlick Run is about 70 feet below. That configuration would make it hard, if not impossible, for rainwater to enter the stream on that side.

Between the houses, Tony Alt keeps the swales grassy and well-maintained. There is a 200-yard buffer zone between the houses and the creek bank behind the houses.

Alt said she was a bit concerned because inspectors thought her bait stations to control rodents were drains. But, she said, the inspectors told her the farm was “well kept up.” She asked what they could do to improve it, she said, and the inspectors said they would send her a letter.

Two months later, Alt received a summary of the report. It talked a bit about possible stormwater discharges, but she still wasn’t concerned.

Then, in November, Alt received a letter from Capacasa stating that she was discharging pollutants into Mudlick Run in violation of the Clean Water Act. If she didn’t apply for a permit in 90 days, she was subject to civil fines of $37,500 per day.

Alt was shocked. She called the West Virginia Department of Environmental Protection. Officials there advised her to do the paperwork and apply for the permit. Even her husband, Tony, told her to apply for it.

So she told EPA she would. But the decision didn’t sit well.

“Nobody could tell me anything that I could do differently. They just said, ‘get this paper.’ Well, what’s this paper going to do to protect the stream?” she asked. “I do enough paperwork as it is.”

When the officials from the West Virginia Farm Bureau heard about her case, Alt invited them to the farm. They could see it was a well-run operation, said Steve Butler, the West Virginia Farm Bureau’s administrator. If Alt’s farm needed a permit, they reasoned, every farm would.

The bureau offered to help her fight the permit. She agreed. On June 14, 2012, one year after the first inspection, Yaussy filed his lawsuit.

The EPA inspectors decided to return for another look at the farm. In December 2012, they rescinded the permit requirement. “Barring a significant change of circumstances or operations at Ms. Alt’s facility, EPA will not issue a similar order to Ms. Alt in the future,” Capacasa wrote.

Alt did make a few small changes in the intervening year, including using a conveyor system to clean out the chicken houses. But, she said, “nothing’s changed at this farm. We still have eight chicken houses.”

Nothing would stop the EPA inspectors from returning the next month, or the next year, and telling her she needed the permit again. And nothing would prevent her neighbors from enduring the sleepless nights that come with threats of whopping civil fines.

The EPA sought to dismiss the case, arguing it no longer had an issue with Alt. But a federal judge rejected that request this spring, saying that the EPA hadn’t changed its underlying position that farms like Alt’s operation needed the discharge permits.

And so the woman who retreated to the rural West Virginia highlands for a quiet life presses on with a federal case that could change the face of agriculture. She fights not just for her neighbors, she said, but for her daughter, a chicken farmer, and her grandchildren, who may inherit her farm someday.

“I believe in standing up for what you believe in,” Alt said. “I knew I wasn’t wrong. I’m still not wrong.”