An appeals court Wednesday upheld a ruling ordering the Environmental Protection Agency to regulate the water discharged from ships as a way to protect local ecosystems from 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 sued the EPA to require it to regulate ballast water because of concerns that invasive aquatic species such as mollusks were being pumped into local waters.

Except for sewage, ship discharges are exempt from regulation. Wednesday's court ruling applies to bilge water and non-sewage wastewater from a ships' showers, laundries, galleys and engines.

While the EPA was appealing the judge's decision, it also drafted regulations requiring oceangoing freighters to dump ballast water at least 200 miles from shore and refill their tanks with new seawater to flush and kill invasive freshwater species.

The agency is taking public comments on the regulations, which would take effect Sept. 30.

"We're reviewing the decision to determine next steps," Benjamin H. Grumbles, EPA's assistant administrator for water said in a 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 Nina 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 such as 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.