Maryland environmental regulators must rewrite a water pollution permit for a troubled, decades-old Eastern Shore plant that recycles poultry scraps, a Dorchester County judge ruled last week.

The Valley Proteins plant in Linkwood has been a source of recurrent concern among environmentalists for years. The facility, which boils waste parts from poultry processing to turn it into pet food, empties wastewater into the Transquaking River, which flows into Fishing Bay and, ultimately, the Chesapeake Bay.

Led by the Chesapeake Bay Foundation, environmentalists and Eastern Shore groups sued the Maryland Department of the Environment last year after regulators granted the facility its first new permit in 15 years, since a previous permit had been extended numerous times despite an original expiration date in 2006.

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Under the ruling issued Friday, a Dorchester County Circuit Court judge found that this new permit falls short of both Maryland and federal law, sending it back to regulators for redrafting.

Judge William H. Jones questioned whether the state’s new permit does enough to reduce the volume of nitrogen and phosphorous that the plant discharges into the Transquaking River. These pollutants exist at high concentrations in poultry products and are drivers of the so-called oxygen “dead zones” that suffocate underwater life in the Chesapeake Bay.

The agency relied on flawed data to back up arguments about the strength of its new permit, while ignoring “real-world, real-time” information, Jones said in his decision.

At the same time, Jones determined, the Department of the Environment used modeling with “questionable status” in scientific communities to measure pollution impacts in the Transquaking and the Higgins Millpond, just downriver from the plant.

“If the Department is to ensure water quality standards, Total Nitrogen and Total Phosphorus limits must guarantee meaningful reductions,” Jones wrote. “As the Permit stands, the Department cannot ensure that is the case.”

In a statement, MDE did not say whether it intends to rewrite its permit for Valley Proteins or appeal the court’s decision. Spokesman Jay Apperson said only that the agency is “reviewing the court’s opinion and order and will respond appropriately.”

The Valley Proteins plant has had repeated issues with pollution in recent years, agreeing to pay close to $1 million a year ago to settle lawsuits by the state and environmental groups, which alleged nearly two years of pollution violations by the facility.

Despite its troubles, the Linkwood plant was purchased two years ago by the Darling Ingredients, a Texas-based food waste company, as part of a $1.1 billion deal for 18 such rendering plants.

A Darling Ingredients spokesperson said in a statement that the company “will respond through the appropriate legal channels.”

Among environmentalists’ grievances with the state’s new permit for the Valley Proteins plant, it would allow the facility to almost quadruple the amount of wastewater it releases into the Transquaking River — from 150,000 gallons a day to up to 575,000 gallons a day — if it took certain measures to rein in pollutants.

The Chesapeake Bay Foundation and Eastern Shore groups that joined the lawsuit against MDE celebrated the outcome and expressed hope that a revised permit can diminish the nitrogen and phosphorous pollution from the plant.

“The court’s decision in this case makes a statement that no river is worth giving up on, and recognizes the value of clean water and in doing all we can to ensure that our waterways are swimmable and fishable,” said Matt Pluta, Choptank Riverkeeper and director of riverkeeper programs for the advocacy group ShoreRivers.

“We are pleased that the court acted on the strength of our arguments and we look forward to a new era of improving water quality on the river,” added Fred Pomeroy, president of the Dorchester Citizens for Planned Growth.

Still, the court didn’t side entirely with the environmental groups. The coalition had urged the court to require Darling Ingredients to make facility improvements “immediately,” but Jones upheld the construction timeline laid out by MDE.

And while environmentalists had called on the court to require regulators to prohibit the storage of waste sludge in places that might risk pollution to waterways, Jones said that this fell under the purview of the Maryland Department of Agriculture, not MDE.

In his decision, Jones invoked the observations of locals who recalled a time when the Transquaking River was teeming with diverse species, “crystal clear” and a “jewel, really.”

But today, said one resident quoted in the judge’s decision, the river looks more like “a nice shade of yuk.”