SAN FRANCISCO – A federal appeals court on Wednesday upheld a ruling ordering the U.S. Environmental Protection Agency to regulate the water discharged from ships often carrying invasive species.

The 9th U.S. Circuit Court of Appeals said it agreed with the federal judge who in 2005 ruled that the EPA exceeded its authority in exempting certain ship discharges from the pollution control requirements of the 1972 Clean Water Act.

A handful of environmental groups and states concerned about the effect of invasive aquatic species like mollusks being pumped into local waters sued the agency to require that ballast water be covered under the act.

Except for sewage, ship discharges have exempt from regulation. Besides bilge water, Wednesday's ruling also applies to non-sewage waste water generated by shipboard showers, laundries, galleys and engines.

While appealing the district court decision, the EPA developed draft regulations requiring oceangoing freighters to dump ballast water at least 200 miles from shore and then to refill their tanks with new sea water to flush and kill invasive freshwater species.

The agency is taking public comments on the proposal, which is set to go into effect on Sept. 30.

“We're reviewing the decision to determine next steps,” Benjamin H. Grumbles, EPA's assistant administrator for water said in a written statement. “It's commonsense and good environmental policy not to require millions of boaters and vessel owners to get Federal clean water permits.”

The ruling comes as efforts to establish a federal standard for cleaning up ballast water have stalled in Congress. Among other issues, California officials have expressed concerns to lawmakers that the state's stricter standards could be pre-empted by a weaker federal law.

Some environmental groups contend the EPA's plan to block foreign species does little to prevent exotics from slipping into U.S. ports and water bodies.

“It's a good first step,” said Niña Bell, executive director of Northwest Environmental Advocates, one of the groups that brought the lawsuit. “But the EPA's got a long way to go when it comes to regulating ballast water.”

Numerous invasive species have devastated aquatic ecosystems throughout the country. In the Great Lakes, global hitchhikers like the quagga mussel and the freshwater ruffe fish out-compete native species for food, spread disease and cost the regional economy billions a year.

Six states, including New York, Wisconsin and Pennsylvania, joined as plaintiffs in the suit. A shipping industry group joined the EPA in fighting the regulations.

Associated Press Writers Mike Gormley in Albany, N.Y. and Erica Werner in Washington contributed to this report.