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From the water, the old wood pilings sticking out of the St. Louis River Estuary appear as ghostlike arms of long-gone industry.

More than 100 years ago, the pilings held buzzing sawmills that helped build this inland sea city. But the byproducts, slipped into the water and out of sight, still haunt: thousands of tons of wood waste covering 75 acres of river bottom, piled 20 feet thick in some spots and inhibiting the natural ecosystem.

This summer, officials with the Minnesota Department of Natural Resources are embarking on a $16 million initiative to restore habitat here. That’s just a fraction of an estimated $300 million to $400 million in projects now underway to restore the 12,000-acre estuary, put onto a list of Great Lakes Areas of Concern three decades ago by an international commission.

The estuary is the primary nursery for more than 40 species of fish in western Lake Superior, including walleye, lake sturgeon, northern pike and smallmouth bass, according to the DNR. It provides habitat for more than 230 species of migrating and resident birds. And increasingly, it’s being viewed by the city of Duluth as an underrecognized natural amenity for locals and tourists.

“This waterway is of statewide and nationwide importance,” said Kris Eilers, executive director of the citizen-based St. Louis River Alliance, which lobbied for cleanup funding. “It’s a unique freshwater estuary. There’s not very many of this size.”

While officials are pleased to see the cleanup accelerating now, decades into the work, it’s clear that cleaning and restoring the mouth of river is a long, bureaucratic and even sometimes tedious process.

A floating excavator’s long yellow arm dipped into the water one morning last week, its red clamshell claw scooping up sediment that had washed into a portion of the estuary known as Kingsbury Bay.

Though not contaminated, the bay has become shallow after years of runoff from urbanization and extreme storms.

This summer, contractors armed with detailed GPS coordinates are removing nutrient-rich sediment scoop by small scoop, loading it into hoppers on barges and floating it downstream to an area known as Grassy Point. There, it is deposited atop the underwater sawmill waste to help bring back aquatic plants and bugs important to the ecosystem. Workers plan to scoop out wood waste in other areas and build an island to shelter a bay for fish and create other kinds of habitat.

The excavator will run six days a week until the season is done, then resume next spring, explained Melissa Sjolund, project manager with the DNR. The scooping and dumping will continue into 2020 at least.

Though the island will be human-made, it will restore the area to more of what it once was, before decades of filling and dredging and dumping, officials said.

“We’re past the point where we can put it back exactly the way it was,” Sjolund said. “We can put back the types of habitat that have been lost.”

Though the estuary’s water is brown with natural tannins from decaying plants, it is already cleaner than it once was, after industry and development polluted it with manufacturing byproducts and even sewage, officials say. Now, monitors are finding that quality fish such as perch, walleye and muskie are coming back to areas they once avoided. Native plants are taking hold, too.

“We’ve talked about this estuary being a crown jewel for Minnesota because it contains this really valuable coastal marsh habitat,” Sjolund said. “It was so heavily used and abused and it is so deserving of ... getting all of this support.”

Still, it will take several years to get the estuary off the Areas of Concern list.

The vast majority of the work has been and will be government funded, said Barb Huberty, the Minnesota Pollution Control Agency’s Area of Concern coordinator. Officials tried to trace pollutants and dumping to specific companies, but many are out of business or have changed hands so many times that a responsible party can’t be identified.

The funding for the estuary, which straddles the Minnesota-Wisconsin border, is complex, Huberty explained. In 2017, for instance, Minnesota legislators committed $25.4 million in state bond money to remediation projects, triggering more than $47 million in federal funding. The state’s Outdoor Heritage Fund is a major contributor to the estuary restoration. U.S. Steel, which used to have a plant on its shores, is contributing about $45 million for aquatic habitat restoration. Other funding is coming from the state of Wisconsin and entities such as the cities of Duluth and Superior.

So far, three out of 10 contaminated sediment sites in Minnesota have been remediated after officials capped pollutants with clean sediment in three boat slips.

Three out of 11 state habitat restoration sites are considered finished as well.

While environmentalists are heartened to see the improvements, some worry that not enough is being done to protect the estuary from future pollutants.

The proposed PolyMet copper/nickel mine is in the St. Louis River watershed, for example, and opponents fear that environmental safeguards could fail, reversing years and millions of dollars of effort.

PolyMet officials have said that state and federal environmental safeguards and modern technology will allow mining while protecting the environment.

In the meantime, the delicate work of cleaning up the estuary will continue. Plans are scheduled as far out as 2024, with hopes of getting it off the list the following year.

Though the public will continue to see heavy equipment and workers in the waterway, much of the result will be out of sight, officials said.

“This is one of the difficulties of doing underwater restoration,” Huberty said. “It looks the same before and after.”

Getting the estuary off the list won’t require pristine conditions, she said, but it will mean restoring the scenic waterway enough that fish and wildlife use it, and people can enjoy it.

“If it took hundreds of years [to contaminate it] we don’t even know how long it will take to recover, so it’s not criteria for delisting,” she said. “We are setting the stage for 100 years from now.”