The Natural Resources Defense Council filed suit on behalf of conservation groups concerned about nitrogen and phosphorus pollution in the Mississippi River basin. High levels of nitrogen and phosphorus can lead to increased algae growth, which can starve waters of oxygen and create so-called dead zones.
Ann Alexander, a senior attorney for the NRDC, said the EPA has stood on the sidelines for too long.
"They have acknowledged the problem for years, but could not muster the gumption to address it," she said in a statement Monday. "The court is telling the agency that it is time to stop hiding from the issue and make a decision already."
NRDC said the suit was filed more than a year ago. It challenges an EPA decision to deny a petition to determine what, if any, action is needed to address nitrogen and phosphorus pollution.
There was no public statement from the EPA.