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A federal appeals court Wednesday upheld a lower court's ruling that boats aren't exempt from Clean Water Act regulation of their wastewater. But that is unlikely to change what's discharged into Alaska waters.

Since 1973, owners of marine vessels haven't had to worry about whether their incidental discharges met federal standards under the Clean Water Act, because the Environmental Protection Agency exempted them.

Discharge "incidental to the normal operation of a vessel" includes sewage, marine engine effluents, and laundry, shower and galley graywater, according to federal code.

But in 2006, the 9th U.S. Circuit Court of Appeals deemed the exemption illegal and ordered the EPA to issue a permit for all marine vessels by Sept. 30, 2008.

The EPA released a draft permit this year limiting the effluents in cruise ships' discharge up to three miles from shore.

Yet large ships here already must meet much stricter state limits, which supercede the federal regs.

"I don't think it will have an effect on the ships that come to Alaska," said John Binkley, president of the Alaska Cruise Association.

Gershon Cohen, a Haines-based advocate of tighter cruise ship wastewater regulation, praised the court's ruling for declaring the original EPA exemption illegal. And he was pleased the EPA must create the framework of a permit regulating cruise ships.

But he also said the new federal permit was unlikely to change how large ships discharge because the requirements are not stringent.

"It's really not going to be much of a burden, frankly," he said.

Small boats needn't worry about stricter regulations, either. Recreational boats, commercial boats under 79 feet and all commercial fishing boats were exempted from incidental discharge regulation this week in two bills passed by Congress.

Alaska's senators and representative voted for the bills.

Recreational boats have a permanent exemption, and commercial fishing boats get a two-year stay on the regulations. Meanwhile, EPA must study the environmental impact of incidental discharges to decide which kinds and sizes of boats should be regulated in the future.

• Contact reporter Kate Golden at 523-2276 or kate.golden@juneauempire.com.