The plaintiffs hope a favorable ruling would force the EPA to implement standards for every state, most of which have only vague limits on such pollution, said Earthjustice attorney David Guest.
The groups say rain sends the runoff, which includes fertilizers and animal waste, into rivers and lakes, contaminating waterways and nourishing algae blooms that poison the ecosystems.
"This is endemic throughout the United States," Guest said. "When you fertilize the water, it makes it so that only one instrument in the ecological orchestra can play. Where you used to have this vast ecological orchestra, now it's only the algae playing."
He said the runoff can also contaminate drinking water supplies and sicken or kill people.
The federal lawsuit was filed in Tallahassee by the Florida Wildlife Federation, the Sierra Club, the Conservancy of Southwest Florida, the Environmental Confederation of Southwest Florida and the St. Johns Riverkeeper.
Guest said the algae blooms are fueled by nutrients from the runoff, which spread throughout waterways, then die and suck up all the oxygen, killing most other life.
EPA said it is reviewing the lawsuit, but noted states should develop their own guidelines.
"It's a priority for EPA to have states adopt science-based numeric standards to control nutrient pollution," EPA Assistant Administrator for Water Benjamin H. Grumbles said in an e-mail Thursday.
Florida's Department of Environmental Protection is still working to set guidelines, which are complex because the agency hasn't determined exactly how much runoff can continue without harming ecosystems, spokeswoman Dee Ann Miller said.
According to the lawsuit, the EPA acknowledged 10 years ago that Florida needed to promptly develop runoff standards to meet the requirements of the Clean Water Act.
The EPA noted in 1998 that "nutrient pollution is the leading cause of impairment in lakes and coastal waterways," according to the lawsuit. At the time, the agency also said the nutrients in runoff had been linked to so-called "dead zones" in the Gulf of Mexico and outbreaks of Pfiesteria, a microscopic organism that lives in estuaries and could harm humans and fish.
Congress enacted the Clean Water Act in 1972 "to restore and maintain the chemical, physical and biological integrity of the nation's waters."
But Guest noted that the Chesapeake Bay, for instance, has been suffering for years from toxic algae blooms caused by water pollution and runoff from development. At times, large swaths of the bay contain so little oxygen that little life remains.
"No other life can live there besides the algae," Guest said. "This is about fertilizing water, and when you fertilize water, algae goes crazy and everything else gets pushed out."