Environmental groups won a major victory this week in their quest to keep invasive organisms out of U.S. waters -- including San Francisco Bay -- in a decision that will force ships to comply with the Clean Water Act when they dump ballast water.

A federal judge in San Francisco ruled that the Environmental Protection Agency can't exempt ship operators when they release ballast water -- a move that could have nationwide implications. Under the Bush administration, the agency had declined to intervene, saying the Coast Guard was a more appropriate enforcement arm. The agency will decide within a month or two whether to appeal.

``This will hopefully be a landmark decision that will dramatically reduce the introduction of invasive species into U.S. waters,'' said Warner Chabot, the San Francisco-based vice president of the Ocean Conservancy, one of the plaintiffs in the case.

Costly problem

Ships take on the extra water to improve stability, but it can bring along foreign critters that can kill native species and disrupt habitats when it's unloaded. If the decision is upheld, ships can be regulated under the federal Clean Water Act as a source of pollutants, much like factories and sewage plants. It's not clear exactly what ships might have to do differently; one option would be to have ships release their ballast water while in the open sea.

The cost of combating the ship stowaways -- which include the Asian clam, European green crab and the New Zealand sea slug -- runs in the billions of dollars each year. Locally, San Francisco Bay has more than 200 non-native plant and animal species, many of which don't have natural predators. The tiny tagalongs kill native species, clog water pipes and disrupt the food chain.

It's hard to reverse the damage, but environmentalists are optimistic the ruling will prevent future invasions and slow the rate at which new species are established. They estimate a new species becomes established in San Francisco Bay about every 14 weeks.

``This is a stunning victory -- the bay-delta-estuary is a poster child for the harm caused by invasive species,'' said Leo O'Brien, executive director of BayKeeper, a plaintiff in the case. ``It's a big enough issue that it will be appealed, but we're confident we'll prevail.''

Tough to enforce

The EPA had previously held that dumping the ballast did not fall under the category of discharging pollutants because it's part of the normal operation of a vessel, said Alexis Strauss, a water division director in San Francisco. ``It looks like EPA's argument has failed here, and we'll have to figure out what to do,'' Strauss said.

The Pacific Merchant Shipping Association, a trade association that represents more than 50 shipping lines on the West Coast, eyed the decision with interest, but spokesman John Berge said the practical implications won't be clear until the EPA sets rules. Already, some states have laws requiring ships to exchange their water en route from international ports, but this move would apply nationwide, as well as to interstate traffic and moves within the state's ports.

But regulations could be hard to pin down, Berge pointed out.

``Because ships are mobile, it's difficult to tell what's in the ballast and what level of pollutant is in it,'' Berge said. ``The permit process to regulate it might be a quandary.''

The judge ordered all the parties to meet for a conference on April 15 to discuss future proceedings.