Scientists have tracked at least 329 invaders in marine environments worldwide; ecosystems have been disrupted from the Great Lakes to San Francisco Bay, where the Asian clam is implicated in a collapse of fish stocks, to Lyttelton Harbor in New Zealand, where an invasive fanworm, a prodigious filter feeder, outcompetes local shellfish.

Yet environmentalists, who have long sought a tough ballast rule, worry that the Coast Guard rule and the other proposals are too weak and that the rollout of enforcement will be far too slow to do much good.

For now, the Coast Guard requires only new ships to install the filtering and disinfecting equipment; others can wait until the next time they enter dry dock for maintenance or repair, which may happen only every five years or so. Because some ships do not fall under the rule until 2016, it could be 2021 before they comply.

“The industry’s had fair warning that this was coming,” said Thom Cmar, a lawyer for the Natural Resources Defense Council who focuses on Great Lakes ecosystems issues. “To give an even further compliance extension on top of what’s already been a long period of delay is unjustified.”

The original proposal by the Coast Guard called for a reappraisal and tightening of standards in 2016; that was dropped, angering the environmentalists and some scientists. They say that onshore treatment plants could be 1,000 times as effective than onboard technology.

Land-based systems could filter ballast with dense and heavy material like sand, they say, a process that is likely to be difficult to replicate on a ship, at least not without crowding out cargo. Most shipboard systems — some 60 have been developed to date — mix and match different filtration methods, usually pumping water through filtered pipes. Then they treat the ballast water with chemicals or ultraviolet light.

The Coast Guard points out that a network of onshore treatment centers for ballast water has not been developed. Even if it were, said Richard Everett, the project manager at the Coast Guard’s Office of Operating and Environmental Standards, “It’s a question of whether we can require a ship to discharge to shore.” Dr. Cohen said he and other colleagues on a panel advising the E.P.A on the issue had told the agency that the panel did not think present shipboard technology to be the best treatment, in part because land-based technologies can be more effective.