A new rule proposed by the federal Environmental Protection Agency would for the first time set a limit on the number of organisms allowed in ships' ballast water discharges.
The rule matches an existing standard set by the International Maritime Organization.
Many destructive invasive species have arrived in the Great Lakes in ballast water from ships.
Duluth Seaway Port Authority spokeswoman Adele Yorde said the rule will simplify things for ocean-going ships that bring cargo in and out of Lake Superior.
"Those vessel operators can now look at one vessel permit that will allow them to transit the entire Great Lakes-St. Lawrence Seaway System and be in compliance with what they're already having to retrofit their ships for to travel to ports around the globe," Yorde said.
Ships that stay within the Great Lakes are exempt for at least four years.
Environmental groups say the limits should be stricter, to protect the Great Lakes from invasive species such as zebra mussels.
Andy Buchsbaum from the National Wildlife Federation said if even a few problem organisms get through, they can explode in population.
"We're seeing progress, but we can't afford to leave door open even a crack to invasive species," Buchsbaum said. "Otherwise we end up with a situation like zebra mussels all over again."
Ship owners say it will cost about $1 million to outfit each ship with control equipment.