A major Seattle seafood-processing company has agreed to pay a $2.5 million penalty and spend millions more upgrading fish facilities throughout Alaska to settle federal charges it violated the Clean Water Act.

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A major Seattle seafood-processing company has agreed to pay a $2.5 million penalty and spend millions more upgrading fish facilities throughout Alaska to settle federal charges it violated the Clean Water Act.

The Environmental Protection Agency (EPA) had accused Trident Seafoods of nearly 500 violations at 14 processing sites over how it handles tens of millions of pounds of fish waste. The company was accused of discharging fish waste without permits, illegally dumping fish waste into national wildlife refuges and creating dead zones in marine waters by discarding fish waste in piles on the sea floor of up to 50 acres in size.

At issue is how Trident disposed of the heads, tails and bones from fish it processed at sea and at shore-based facilities from St. Paul to Cordova, Sitka and Ketchikan. EPA officials said the company killed marine life by allowing decaying fish waste to pile up over years and create dead-zones waters at sites throughout Alaska.

In one area, the fish waste has piled up underwater into a “massive carpet of gelatinous goo that suffocates sea life and disrupts the entire ecosystem in that area,” said Tara Martich, permit coordinator with the EPA.

“Trident’s facilities have had a long history of noncompliance,” she said. “We know through monitoring that the company’s piles are still there sometimes decades later.”

The violations initially came as a surprise to Trident’s leadership, said Joe Plesha, the company’s chief legal officer, who said lower-level employees weren’t following the letter of the law. He said the company takes responsibility for its failures, which occurred from 2005 to 2009, and has since increased its internal auditing.

According to a settlement agreement filed Wednesday in U.S. District Court in Seattle, Trident also will spend at least $30 million to better manage its fish waste in Alaska.

In Naknek, the company expects to build a plant that will safely dispose of 30 million pounds of waste by grinding it into fish meal that can then be sold as protein to fish farms.

Federal officials said the changes should reduce Trident’s waste discharges by more than 100 million pounds a year.

EPA officials said they hope changes at Trident, one of the largest fish-processing companies in the world, with 8,000 employees, will encourage other processors to do more to better manage fish waste.

“One of the reasons we’re bringing these enforcement actions is to point out to the seafood industry that we’re really looking at these types of issues,” said Ed Kowalski, director of compliance and enforcement for EPA’s Northwest region.

Craig Welch: 206-464-2093 or cwelch@seattletimes.com