The federal agency has made clean-up a priority, but a local group of "waterway watchdogs" isn't waiting for the EPA to act.
Every week, a group called the Puget Soundkeeper Alliance goes on the hunt for polluters.
"Part of being a water keeper means having a boat and going on patrol on your watershed," said Chris Wilke, the group's executive director.
The non-profit organization is hunting polluters, and they have a good track record of finding them. Since 1984, the organization has reached more than 100 settlements with polluters of Puget Sound waterways worth $3.7 million.
"If there is any penalty element, we always award that to a third party organization that will keep the money here locally," Wilke said. "It will go into restoration and water quality work in this watershed."
Wilke said that's the benefit of a citizens' group filing federal complaints. When the EPA does it, the settlement money goes into federal coffers.
The most common worry is industrial stormwater runoff, which Wilke said used to be a problem at the Alaska Marine lines. But thanks to pressure from the Alliance, Alaska Marine now has its own on-site stormwater treatment.
It's one of at least a dozen examples of the Alliance's efforts on the Duwamish and represents another step toward cleaning up one of the most polluted rivers in the county.
"We have a right to expect this area to be clean, to support aquatic life and be able to go fishing and eat the fish," Wilke said.
In addition to patrolling the waterways, the organization also learns about potential violators through public records requests. They also have a tip line at 1-800-42-PUGET.