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For a century, we have straightened, poisoned, dug, soiled, filled and recontaminated the Duwamish River, the freshwater corridor that transformed Seattle into a major port city.

We buried old trucks and tossed in piles of oil-soaked tires. We dumped carcinogenic lubricants and coolants down drains and let solvents seep deep into its muddy bottom.

But on Tuesday — after 14 years of research and planning — the federal government unveiled a final $342 million cleanup plan that officials insist should rid the beleaguered waterway of 90 percent of its pollution.

The full effort will take nearly two decades, with costs borne by Boeing, King County, and the city of Seattle and the Port of Seattle.

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But Obama administration officials said the results will allow residents of South Park to safely eat more food from the river, while letting tugs and other businesses still work the Duwamish as an industrial waterway.

“I think we’re delivering a plan that is as aggressive a plan as can be done,” said Dennis McLerran, regional administrator for the Environmental Protection Agency (EPA), which oversees the Duwamish cleanup.

“This is a carefully thought through, technically sound approach that we believe will leave us with the cleanest possible river we can get,” he said.

The EPA will require 105 acres of river bottom to be dug up, removing nearly 1 million more cubic yards of polluted earth to landfills.

Two dozen other acres of contaminated river bottom will be capped beneath several feet of rock, sand and carbon, while other, less-damaged areas will be covered with less than a foot of new earth and mud.

Time and the river’s natural tendency to push fresh sediment downstream from above will be used to restore another 235 acres.

Timing of restoration work will be flexible to allow businesses to continue operations.

Some early projects costing roughly $150 million have been under way for years, and are expected already next year to reduce by half one of the river’s more menacing pollutants — polychlorinated biphenyls (PCBs), chemicals once found in everything from hydraulic fluids to lighting fixtures.

But PCBs, which are damaging to internal organs and can work their way up the marine food chain to creatures eaten by humans, are just one of the many pollutants threatening the river.

Long-term cleanup also will focus on arsenic and other compounds.

The waterway’s Dungeness crab, clams, perch and sole, which health officials now consider too dangerous and filled with toxins to eat, will be monitored and tested as one measure of how well the cleanup is working. But nobody will be fined or punished if fish aren’t getting clean fast enough, officials said.

“There are so many dynamics in a large river system like this one,” said Lori Cohen, with EPA’s Superfund program in Seattle. “We expect that the fish-tissue contamination levels will decrease. But it’s very difficult to tie sediment cleanup in a direct correlation to those fish-tissue levels being reduced.”

Allison Hiltner, who manages the cleanup for EPA, said it’s unlikely that people will ever be able to eat unlimited quantities of all fish and shellfish from the Duwamish, but added that even healthy streams around Puget Sound still have some health-related fish advisories.

“We’re going as far as we think is going to be possible in this urban waterway,” she said.

In fact, the Washington Department of Ecology is still working on a massive effort to identify and clean up ongoing sources of pollution to make sure the river won’t be recontaminated after EPA’s goals are met.

Since the troubled river was listed as a Superfund site in 2001, debate over how — and how much — to restore it has been bitter, with community members and adjacent businesses, tribes, Boeing and local governments rarely pulling for precisely the same plan.

On Tuesday, representatives of a neighborhood group that has bird-dogged restoration for years said the plan was better than they expected in the wake of lobbying by business interests.

“EPA is holding everybody to water-quality standards and sediment standards that are very high, still,” said James Rasmussen, with the Duwamish River Cleanup Coalition. “We were worried that that would change.”

Said BJ Cummings, policy adviser for the same community group: “It’s an improvement. It removes more toxic waste than EPA previously proposed. It helps reduce long-term risks to people who live and fish there. But what they are requiring still doesn’t go far enough.”

While Seattle Mayor Ed Murray dubbed Tuesday a “huge day for Seattle’s only river,” Boeing officials and King County Executive Dow Constantine were more opaque.

Boeing released a statement saying it was reviewing EPA’s decision “in hopes that it will build upon the solid progress that has been made over the last decade.”

Constantine called it a “complex decision” his office “must review closely.”

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