The state Department of Environmental Protection has filed a lawsuit against Reliant Energy's Conemaugh Generation Station for polluting the Conemaugh River, even though the agency has a rare, and until recently, unpublicized agreement with the company that allows it to discharge pollutants into the river.

At the same time, the DEP also has proposed renewing the discharge permit for the coal-fired power plant in Indiana County, but plans to amend it to eliminate the water pollution limits that were violated hundreds of times in the past two years. Those water pollution limits are the same ones that the department is seeking to enforce in its lawsuit.

The department's seemingly contradictory positions, in court and on Reliant's permit renewal, may effectively put an end to a federal lawsuit by environmental groups seeking enforcement of the power plant's original water pollution limits.

"This doesn't smell good," said Josh Kratka, a National Environmental Law Center attorney who filed a federal lawsuit on behalf of the Sierra Club and PennEnvironment, alleging that the power plant has been, and remains, in regular violation of the federal Clean Water Act.

According to that lawsuit, which was filed April 10 in U.S. District Court in Pittsburgh, Reliant discharges 3 million gallons of wastewater a day into the river. That wastewater regularly contains potentially toxic levels of selenium, manganese, aluminum, boron and iron. Selenium, in particular, is highly toxic to fish and waterfowl.

The environmental groups have said that continued power plant discharges will impede ongoing efforts to restore the Conemaugh River, which has a long history of industrial and mine pollution and has been designated an "impaired water body" by the DEP. The power plant's water pollution discharge limits were originally established to protect the river.

But the permit was appealed by Reliant in 2001, and the DEP agreed to waive enforcement of the water pollution discharge limits for 10 years, until 2011.

The DEP said the waiver was granted because the air pollution control equipment installed at the power plant in 1994 and 1995 was collecting more pollutants than the power plant's water treatment facility could remove. Effectively, some of the pollutants removed from the air were discharged into the river.

Pat Hammond, a spokeswoman for Reliant, which owns the 1,711-megawatt power plant in partnership with seven other companies but is its sole operator, said the company also found the agency's legal position curious.

"We are in compliance with the [side] agreement we had with the DEP and believe this action before the court will affirm the agreement," Ms. Hammond said. "We continue to work toward improving water quality in the state and are committed to resolving this as quickly as possible."

The DEP lawsuit, filed April 5 in Commonwealth Court in Indiana County, under federal environmental law takes precedence over the lawsuit filed by the environmental groups.

Citizens and interested parties may file lawsuits when an environmental agency is perceived to be failing to do its job. But if an agency can show that it is enforcing its regulations, then a complaint may be considered moot.

Mr. Kratka said the DEP did not inform the environmental groups that it had filed its state lawsuit, and the agency did not issue a news release.

"On one hand the DEP filed a lawsuit to enforce the current permit and preclude our lawsuit, while at the same time its trying to eliminate the pollution limits from the [renewed] permit," said Mr. Kratka. "Is the DEP trying to enforce or eviscerate the permit?"

He said the DEP's draft permit renewal, which proposes eliminating the discharge limits contained in the 2001 permit, is a violation of the Clean Water Act and state rules against "backsliding" -- that is allowing pollution discharges to increase instead of working toward their eventual elimination as required by federal law.

Helen Humphreys, a DEP spokeswoman, defended the department's legal action against Reliant.

"We believe strongly that the DEP should lead on this issue and believe that there should be a resolution that is satisfactory to the department and the other parties involved," Ms. Humphreys said.

She said the final form of the permit renewal also will be part of negotiations to settle the enforcement action.