Ruling in a bitterly contested case with national ramifications, a federal judge found Thursday that the Waterkeeper Alliance failed to prove that an Eastern Shore farm's chicken houses were polluting a tributary of the Chesapeake Bay.

U.S. District Court Judge William M. Nickerson declared in a 50-page opinion that the New York-based environmental group had not established in a two-week trial in October that waste from chicken houses owned by Berlin farmers Alan and Kristin Hudson was fouling a drainage ditch that ultimately flows to the Pocomoke River.

He also rejected arguments that Perdue, the Salisbury-based poultry company for whom the Hudsons raise birds, should share responsibility for any pollution because of its tight oversight of contract chicken growers.

Alan Hudson, flown by Perdue with his family to a news conference in downtown Baltimore, said he and his wife were relieved by the verdict, which came three years after the environmental group first publicly accused their Worcester County poultry operation of polluting a waterway.

"It's been very trying for us,'' he said with his wife and two young children beside him, "but we're glad it went this way and we can get on with our lives."

Spokespeople for the Waterkeeper Alliance and for the University of Maryland environmental law clinic, which represented the group, said they were disappointed by the judge's ruling and are considering an appeal. They said they believed they had raised important issues about farm pollution and the adequacy of government environmental protection.

The case attracted national attention, as environmental and agricultural industry groups alike saw it as a major test of whether poultry companies like Perdue can be held legally accountable for any pollution from the waste the birds generate.

The companies own the birds and supply all feed but insist they are not responsible for dealing with the waste. Perdue subsidized a public-relations campaign, savefarmfamilies.org, to publicize the Hudsons' case and helped with raising funds to pay their legal bills.

"Perdue and the Hudsons were convenient targets in the Waterkeeper Alliance's national campaign against modern agriculture," Perdue spokeswoman Julie DeYoung said in a statement. "The Assateague Coastal Trust and University of Maryland Environmental Law Clinic were enthusiastic partners in this reckless witch-hunt against Maryland farmers," she added.

The trust is a member of the Waterkeeper group, and the university's clinic drew criticism from farm groups, rural lawmakers and even Gov. Martin O'Malley for their role in the case.

Though the ditches draining the 300-acre farm were contaminated at the time with high levels of bacteria and nutrients typically found in animal waste, Nickerson wrote that the Waterkeeper group had only shown it was "possible" some of the pollution had come from the Hudsons' two chicken houses holding 80,000 birds.

The group argued that waste was blown out of the chicken houses by large ventilation fans and tracked out by equipment and boots, then washed off the farm whenever it rained.

The judge indicated he was convinced the contamination came from the farmers' herd of 42 cows, which evidence showed roamed about the farm and deposited manure near the drainage ditch. Runoff from livestock in such circumstances was not regulated at the time, though the Maryland Department of Agriculture has since adopted rules requiring that farm animals be kept away from water.

Given the ton and a half of waste estimated to be generated daily by the cows, Nickerson faulted the Waterkeeper group and its legal team for not sampling the vent fans and the ground around the chicken houses for traces of manure.

The ruling was welcomed by farm groups that had rallied in support of the Hudsons.

"Today's ruling is a win for Delmarva's family farmers and against radical environmental activists who disregard the facts, sue first and ask questions later," National Chicken Council president Mike Brown said in a statement.

It was also hailed by Perdue, whose lawyers had contended that the lawsuit threatened the modern poultry industry, in which farmers raise chickens under contract to companies like Perdue, Tyson's and Mountaire.

"They want to change the contract relationship," Steve Schwalb, Perdue's vice president of environmental sustainability, said at the press conference.

The Waterkeeper Alliance and some other groups contend that the system unfairly dumps responsibility for dealing with the birds' waste on farmers, and that poultry farm runoff is a major polluter of the Chesapeake and other waterways because of lax government oversight. It had hoped through this case to make companies take legal and financial responsibility for dealing with the millions of pounds of waste chickens generate on the Delmarva Peninsula and in other poultry-growing regions.

The group had argued in its lawsuit that Perdue should be required to share legal responsibility for any pollution from the Hudsons' farm because the company effectively controlled the raising of the flock, inspecting the houses frequently, issuing orders to the growers and at times adjusting the operation.