The Justice Department and Environmental Protection Agency said the alleged violations resulted in partially treated sewage, with pollutants such as fecal coliform bacteria at higher-than-legal limits, being discharged into South Unalaska Bay.
The bay is listed as an impaired water body, too polluted or degraded to meet state water quality standards, and is home to some endangered or threatened species.
The complaint seeks tens of thousands of dollars a day in penalties for alleged violations dating to 2004. Federal attorneys, in their filing, said that "upon reasonable opportunity for further investigation and discovery," evidence would show permit violations past October.
Unalaska city officials said they hadn't seen the complaint Thursday afternoon and didn't have immediate comment.
State Assistant Attorney General Cameron Leonard said the filing wasn't entirely unexpected. Federal, state and local officials have been talking for months on whether they could settle the matter, he said. The city believes there were errors in the permit under which it has been operating, Leonard said.
He said there's "no question" there have been some violations, though he couldn't say whether the number cited in the complaint is accurate. From the state's perspective, the matter hasn't represented a public health threat, Leonard said.
The state is listed as a defendant, a requirement under the Clean Water Act.
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