Environmental organizations say they have won a battle this week in the effort slow the spread of invasive species in the Columbia River, Great Lakes and other ports of call.

"The decision really does apply uniformly across the country," Nina Bell said of an appellate court opinion issued Wednesday that declared illegal regulations that allow certain ship discharges without Clean Water Act permits. The exempt discharges include effluent from properly functioning marine engines; discharge of laundry, shower, and galley sink wastes from vessels; and any other discharge incidental to the normal operation of a vessel, including the discharge of ballast water.

Bell, of Northwest Environmental Advocates, says those discharges have contributed greatly to non-native species invasions in the United States and elsewhere that are disrupting native plant and animal life.

The decision affirms a 2005 lower court ruling that gives the Environmental Protection Agency until September to end the regulatory exemption and issue permits to ships. EPA had appealed that decision to the U.S. Court of Appeals for the Ninth Circuit.

The challenge was brought by Northwest Environmental Advocates, San Francisco Baykeeper and The Ocean Conservancy, three of the signers of a petition filed with EPA in January 1999. EPA denied the petition in 2003, triggering the lawsuit. The states of Illinois, Michigan, Minnesota, New York, Pennsylvania, and Wisconsin joined the lawsuit as plaintiffs-intervenors.

Those states and Canada surround the Great Lakes, which have in recent decades had profound and costly problems associated with invasive species. Preliminary data released last week by researchers at the University of Notre Dame estimate that invasive species that arrived in the ballast tanks of ocean-going vessels may be causing the Great Lakes region upwards of $200 million dollars a year in losses to commercial fishing, sport fishing, and the area's water supply. That estimate does not include Canadian losses.

The invaders include zebra and quagga mussels, first discovered 20 years ago and now spread across North America as far as Nevada and California, as well as more recent invaders such as the Eurasian ruffe, round goby and spiny water flea.

Eurasian ruffe compete with yellow perch and walleye, reducing populations, round goby are voracious benthic predators, preying on smallmouth bass nests, and zebra and quagga mussels are responsible for substantial biofouling, and altered water clarity and energy flows, according to researchers. Together the foreign creatures have upended the Great Lakes ecosystem, greatly reducing numbers of native fish stocks.

Another recent survey estimates $268 million in zebra mussel-related impacts just to drinking water and power plant facilities from 1989 to 2004 in the Midwest and East.

The mollusks can clog water-intake systems at power plants, irrigation districts, public water suppliers, and other facilities.

Officials from the Northwest have been watching closely the spread of quagga mussels westward.

There is concern the mussels will raise havoc with expensive instruments attached to Columbia basin dams that are intended to improve salmon survival, like fish ladders and screens, and juvenile passage systems.

Portland State University researcher Mark Sytsma said Thursday that the quagga mussels could well arrive in the Northwest, but their most likely mode of transport would be recreational boats.

Ballast water is taken up in one port to help stabilize a light or empty vessel, and is transported to another port and discharged as the vessel is loaded with cargo. Discharged ballast water includes aquatic nonindigenous organisms that can become established in the receiving water.

Oregon and Washington law requires that that ballast be exchanged in the saltwater before entering the river, not in the Columbia or Willamette rivers or at five lower Columbia ports.

A research survey of introduced species in the lower Columbia River carried out in 2001-2004 catalogued 269 species. Of the total, 21 percent , 54 (21 percent) were introduced, 92 (34 percent) were native, and 123 (45 percent) were cryptogenic. The Lower Columbia River Aquatic Nonindigenous Species Survey was carried out by Sytsma and Robyn C. Draheim of PSU, Jeffery R. Cordell of the University of Washington and John W. Chapman of Oregon State University. Sytsma heads PSU's Center for Lakes and Reservoirs.

The majority of the introduced species were fish (28 percent), aquatic plants (23 percent) and crustacea (15 percent). The remaining 18 percent was a combination of mollusks, annelids, bryozoans, cnidaria, amphibians, reptiles and an aquatic mammal, according to the research report

Most of the new fish species were introduced intentionally and didn't enter the Columbia aboard a ship. But many of the introduced plants in the lower Columbia did likely get flushed into the river in ship ballast, Systma said.

"The dominant species are from Asia," Systma said of the aquatic fauna in the lower river.

That puts the ecosystem in precarious position. Some of the non-native plants and invertebrates could provide the same function in the food chain as the native species they replaced. But they may not.

"We've already modified the Columbia River in a lot of ways" from its natural state, Systma said.

The research sampled 134 sites from Bonneville Dam down to the river mouth. The sites included brackish and freshwater marshes, low salinity mudflats, polyhaline beaches, rocky shorelines, protected embayments, large river habitats, tidally influenced agricultural drainages, and urban sloughs.

More than 21 billion gallons of ballast water from international ports is discharged into U.S. waters each year. The cost of damage caused by invasive species to the U.S. economy overall is estimated in the billions of dollars annually, according to the plaintiffs in the lawsuit.

The court's ruling upholds the lower court's order directing EPA to take specific action to ensure that shipping companies comply with the Clean Water Act and restrict the discharge of invasive species in ballast water. In mid-June, EPA issued a draft permit to regulate all vessel discharges. The draft permit requires treatment of a wide range of pollutants contained in ballast water and many other types of ship discharges.

Numerous states have passed their own pollution control laws.

Michigan and Minnesota require shippers to have discharge permits. California has the strictest controls on the discharge of ballast-borne invasive species in the world.

The six Great Lakes states – New York, Michigan, Pennsylvania, Illinois, Minnesota, and Wisconsin – joined the environmental groups' lawsuit to persuade the court to require a federal regulatory program.