Long before a federal judge in Baltimore issued his verdict in the case of the Waterkeeper Alliance vs. Alan Hudson and Perdue Farms, many environmental advocates on the Eastern Shore felt they had already lost.

Groups that work closely with farmers and the poultry industry saw no upside to the case. Not in the idea that one of their own had filed a lawsuit against a family farmer. Not in the fact that the Waterkeepers had gone after Perdue, which has undertaken initiatives to reduce the pollution generated in the chicken-growing process. And certainly not after state authorities determined the pile that spurred the lawsuit was not poultry manure, but instead sewage sludge, leaving the Waterkeepers to base their case on small amounts of manure tracked in and out of the poultry houses and blown out by fans.

"They made a huge mistake," said Mike Pretl, a longtime attorney who has been active in Wicomico County environmental issues. "It definitely sets us back…they should have backed off when they realized they pointed the finger at the wrong litter."

The decision to go forward even as the facts changed in the poultry case may make it harder for Pretl and his fellow environmental advocates to work with farmers on preserving land, planting cover crops and turning manure into energy.

It may have far-reaching political consequences—the University of Maryland's Environmental Law Clinic represented the Waterkeeper Alliance, and clinic leaders drew a harsh rebuke from Maryland's governor for assisting a New York-based group in its case against a Maryland farm family.

It may have broad implications for future legal action against large-scale poultry growers. And, if the judge awards attorney's fees to Perdue and the Hudsons, the case may scare environmental groups from future citizen suits against polluters.

"I'm kind of holding my breath as to what is going to happen," said Pat Parenteau, senior counsel to the Vermont Law School's Environmental and Natural Resources Law Clinic and a former regional counsel to the EPA. "Hard cases make bad law, and that's the lesson on this case. If I'm a lawyer in front of a judge arguing another Clean Water Act case, I'm going to say the outcome here is site-specific, to this farm and these allegations. But the truth is, a loss is a loss."

It's hard to imagine a more complete loss than the one that the Waterkeeper Alliance and the Maryland law clinic sustained, from a legal and public-relations perspective.

First, while many environmental groups use litigation as a last resort, the Waterkeepers let it be known they were looking for a test case that would hold poultry companies responsible for pollution discharges from their contract growers. Currently, the companies exercise much control over the growing process, but they leave the farmers with the manure. Farmers like that—they can use the manure to fertilize their crops, or sell it to their neighbors. But environmentalists don't, because nitrogen and phosphorus in the litter adds to the loads going into rivers and the Chesapeake Bay.

Fresh from successful litigation over hog farm practices in North Carolina, the Waterkeepers boarded a plane in late 2009 to fly over the Shore's poultry houses and find their case. On the plane were Assateague Coastkeeper Kathy Phillips, Waterkeeper Alliance attorney Scott Edwards, North Carolina riverkeeper Rick Dove and a Wall Street Journal reporter. From the air, the group spotted and photographed what appeared to be a pile of chicken manure on the Hudson Farm near Berlin, MD. When Phillips later tested the water in ditches leading from the farm, she found high levels of E. coli and fecal coliform.

That led to their second mistake: Talking about the giant pile of manure. Phillips and the Waterkeepers criticized the state's departments of environment and agriculture for lax rules and infrequent inspections that led to farmers piling their chicken manure without regard for how it polluted waterways. But several longtime residents quietly told reporters that the pile wasn't manure, and eventually the Maryland Department of the Environment confirmed it was treated sewage sludge from Ocean City.

Regulators ordered Alan Hudson to move the pile and fined him $4,000—but an administrative law judge overturned that decision, saying Hudson broke no laws in keeping the pile uncovered. At that time, there were no regulations for storing biosolids, just recommendations. The judge scolded Hudson for not following best management practices, but concluded he broke no laws.

The third problem occurred when the case lost its local clients. Phillips, the Assateague Coastkeeper (which was Phillips' official position) and the Assateague Coastal Trust (which hired Phillips as the Coastkeeper) were original plaintiffs, along with the Waterkeeper Alliance, Inc., based in New York. The judge removed Phillips, the Assateague Coastkeeper, and the Assateague Coastal Trust as plaintiffs because their addresses had not been properly entered in the filing. This left the Waterkeepers as the sole plaintiff and fueled perceptions that an elite, New York-based group that regularly held fund-raisers at ski resorts and counted Kennedy-friendly celebrities among its membership was going after a hard-working family farmer and a longstanding Maryland company. Local legislators who are often supportive of environmental causes did not know these plaintiffs, and neither did fellow environmentalists.

Meanwhile, Scott Edwards, who was familiar with Chesapeake issues and had been instrumental in the Waterkeeper's bringing the suit, left the organization to begin an environmental practice at Food and Water Watch, another environmental advocacy group.

With Phillips off and Edwards relegated to an occasional consulting role, the University of Maryland Environmental Law Clinic became the primary driver in the case. Jane Barrett, a seasoned environmental attorney, took a lead role. Her work brought to light that Alan Hudson had not filed a nutrient management plan from 2003 to 2008, despite a law requiring him to; that he had not kept track of the manure he'd spread until 2008; and that he had never conducted a soil test on his farm, despite requirements that he do so every three years.

But U.S. District Judge William Nickerson seemed unmoved. He focused on Phillips' erroneous claims that the pile was chicken manure. And he was not happy that the Waterkeepers and Phillips were looking for a test case to establish a precedent for integrator liability.

"Plaintiff's case has now gone from a large pile of uncovered chicken manure to small amounts of airborne litter from the exhaust fans, trace amounts brought out on shoes and tires, and a dustpan of litter left on the heavy use pads," Nickerson said in his April order that denied summary judgment to Perdue and allowed the case to go forward, but was full of warnings to the plaintiffs.

In the end, the Waterkeeper's central argument that ventilation fans had provided the pathway for the pollution found in the ditches would not be a convincing one for Nickerson. Instead, he said in his ruling, it was more likely that manure from Hudson's 90 cows had fouled the water.

The misidentified pile, it seemed, had not just cost the plaintiffs goodwill, but also much of their case. A cause-and-effect argument of a large pile of manure and pollution in a ditch would have been much easier to prove than the "trace amounts" of manure and dust coming off fans and shoes, attorneys said. The plaintiffs did not advance the theory in court that the pollution could have come from the sludge; treated waste can leach into waterways, but not likely to the extent of the readings in the ditch, according to environmental officials. Plus, it would be hard to show how Perdue was responsible for the sewage sludge, which was delivered under an agreement between the farmer and the Ocean City plant.

The plaintiffs found themselves without much support from the usual places—liberal Democrats and fellow activists. But it got worse when lawmakers threatened, unsuccessfully, to strip the clinic of its funding. Gov. Martin O'Malley also wrote a letter to the law school's dean, criticizing the clinic's decision to represent the Waterkeepers and suggesting that they would be more true to their mission if they helped the farmer.

Meanwhile, a group called Save Farm Families, with help from Perdue's public relations firm, organized chicken dinners to help Alan Hudson pay his attorney's fees. In a video on the website, Alan Hudson and his wife, Kristin, talked about the toll the suit was taking on their two children. The farm community rallied to support them.

Now that the Waterkeepers have lost the case, environmentalists who work with farmers and Perdue worry they have lost trust it took so long to build. This is particularly so for Chesapeake region Riverkeepers who are affiliated with the New York alliance but were not part of the lawsuit.

"There are a lot of people who misunderstand the relationship," said Tim Junkin, executive director of the Midshore Riverkeeper Association and himself a well-known litigator and author. "We had absolutely nothing to do with that case. We're not going to let it stop us from trying to be successful with our work."

Judith Stribling, a biology professor at Salisbury University and the founder of Friends of the Nanticoke, was one of the few environmentalists who criticized the suit from the beginning. Stribling, who moved to the Shore in the 1970s, remembers when chicken carcasses were dumped in the open and packs of feral dogs and turkey vultures roamed, devouring the meat. Farmers spread chicken waste year-round, even on frozen ground, and no one used sheds to store manure.

"It's hard for me to imagine that the nutrient inputs from poultry have not gone down dramatically since those days, because so much has been done," Stribling said. "Maybe it's not nearly enough, but it's so much more than used to be done."

Laws helped change those practices. But Perdue was also a leader in steering the industry toward cleaner methods, Stribling said. Perdue was the first of the chicken companies to ban arsenic in its feed. In 2000, it built a plant in Delaware to recycle poultry litter into a soil additive, and now takes 10 percent of its growers' manure. Perdue executives have sat on the boards of various Bay organizations, among them the Oyster Recovery Partnership and the Alliance for the Chesapeake Bay.

In 2008, the company entered into a voluntary agreement with the EPA to evaluate the company's largest growers and advise them on the best ways to limit discharges. Perdue considered the program a success but suspended it in the wake of the lawsuit because the Waterkeepers said it was evidence of Perdue's control over its growers. In his ruling, Nickerson chastised the Waterkeepers for using the program against Perdue and said he hoped the company would resume it.

Steve Schwalb, Perdue's vice president of environmental sustainability, said the company hopes to do that. Schwalb said that Perdue never stopped working with what he calls "reasonable environmentalists."

"You got farmers who now question any trust with environmental organizations. And we work hard to say, 'don't lump the regional ones with the fringe group.' And we view the Waterkeepers as a fringe group," Schwalb said.

If those farm relationships become further strained, perhaps no group has more to lose than the Chesapeake Bay Foundation. Its efforts include securing federal funding for conservation practices and helping farmers implement them.

"The two communities, there's not a lot of trust going in either direction. We have been successful in breaking down some of that, really working farmer to farmer," said Kim Coble, the foundation's vice president for environmental protection and restoration. "But at the community level, that trust issue goes both ways and continues to be a struggle."

In the past, the foundation has sued Philip Morris, the EPA and the owners of a Baltimore steel mill over pollution. But it was not asked to join in the Waterkeepers suit, and it wouldn't have in any case, said its senior attorney, Jon Mueller.

Because Nickerson said the plaintiffs failed to prove a discharge from the regulated poultry growing operation, he did not spend a lot of time in his ruling discussing Perdue's liability. He did say that in his opinion, but not as a finding of law, the "type of control exercised by Perdue does not provide a basis for imposing CWA liability."

Mueller, of the CBF, said that he hopes future judges will note that Nickerson's conclusions were "dicta," a legal term for an opinion that is reasoned but not binding, and will also consider the opinion to be site-specific.

More troubling to Mueller is Nickerson's earlier warning that he might be willing to assess the defendants' attorney's fees to the plaintiffs. Perdue has asked for $3 million; Hudson sought about $500,000.

"That kind of money would wipe out most citizen organizations," he said.

As Nickerson noted in his summary judgment ruling, assessing attorney's fees in Clean Water Act cases is rare, but not unprecedented. In 2006, a Colorado judge ordered the Sierra Club to pay more than $300,000 to two mining companies after a lawsuit over pollution lasted more than five years and the judge ruled in favor of the defendants.

That Sierra Club case "should have been a wake-up call for a lot of people," said Parenteau, who has been teaching the Waterkeeper case in his law classes and said the case "scares my students to death."

Parenteau counsels negotiation—four of the stormwater cases the Vermont clinic brought last year settled quickly. And he also tells students that the easiest cases to win are the ones where there are a permitted operation and paper proof of a violation. A possible illegal discharge case where a permit hasn't been issued is much harder to prove. That was the case with Hudson, as the state was still reviewing his and others' CAFO permit applications.

"The citizen groups that file these cases had better sit up and take notice," Parenteau said. "For cases like this going forward, you better build in from the beginning a process to say, 'I think the prudent thing to do is withdraw from this field and fight another day.' "