SAN FRANCISCO (AP) – A federal judge ruled the government can no longer allow ships to dump without a permit any ballast water containing nonnative species that could harm local ecosystems.

U.S. District Judge Susan Illston ordered the Environmental Protection Agency to immediately repeal regulations exempting ship operators from having to obtain such permits.

“This is a slam dunk for healthy oceans,” said Sarah Newkirk, clean water advocate for the Washington, D.C.-based Ocean Conservancy. “The court decision will prevent a vast amount of pollutants from the shipping industry from entering U.S. waters.”

EPA officials did not immediately return calls seeking comment.

In 1999, the Ocean Conservancy and four other environmental groups petitioned the EPA to repeal the ballast-water exemption. They claimed the Clean Water Act prohibits the discharge of pollutants, including biological materials – such as invasive species – into U.S. waters without a permit.

When the EPA denied the petition, the conservation groups filed a lawsuit in federal court in San Francisco in 2003.

Invasive species are known to cause significant economic and environmental damage. Marine species such as mollusks often are inadvertently transported in the ballast water of ships and discharged at ports far from their origins.

The bay’s two most destructive species that originated in ballast water are Chinese mitten crabs, which clog irrigation and drinking water pipes, and Asian clams, which consume large amounts of plankton at the expense of other marine species.

Invasive species in San Francisco Bay cause more than $40 million in economic damage each year, Newkirk said.