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Sometime over the next several weeks, the Muddy River will be unearthed from its stretch of underground pipes and once again allowed to run freely above ground from the headwaters of Jamaica Pond to the Charles River.

The long-delayed US Army Corps of Engineers project will restore a broken watery link in the Emerald Necklace — the graceful chain of parks that runs along the river’s banks from Boston Common to Franklin Park — and reduce the risks of flooding in the Fenway and Brookline, officials say.

Some local officials are worried that the $61 million restoration project doesn’t go far enough. Margaret Dyson, director of historic parks for the Boston Parks and Recreation Department, is among those who favored a more ambitious effort.

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But that concern didn’t temper her elation on a recent morning as she watched excavators and bulldozers dig the channel where the water will soon flow.

“This is huge — exciting,” said Dyson, with tears in her eyes. “We’re seeing sights that we haven’t seen since the 1920s.”

The work, which has rerouted traffic in the congested area six times since the project began, includes massive new culverts to carry the Muddy beneath the Riverway and Brookline Avenue.

The project seeks to prevent the kind of flooding that devastated the neighborhood in the fall of 1996, when the Muddy swelled beyond its banks and inundated the MBTA’s Kenmore Square station, the Museum of Fine Arts, and Northeastern University. The federal government is paying 65 percent of the costs, while Boston, Brookline, and the state are covering the rest.

Work includes dredging some of the river, removing invasive reeds, and the so-called “daylighting” of the 700 feet of the Muddy that is now buried beneath a windswept lot across from the Landmark Center.

The Army Corps originally planned a more extensive project that would have included dredging up large amounts of sediment from the Fens, Riverway, Leverett, Willow, and Wards ponds, eradication of all the invasive tall reeds, and far more environmental restoration. But Corps officials estimated it would cost an extra $800,000 an acre for the additional work, which they decided was too much.

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“We have huge concerns,” said Julie Crockford, president of the Emerald Necklace Conservancy, who fears that the work won’t be enough to prevent flooding from the increased precipitation that climate scientists expect the region will experience in the coming years.

She also said she worries that the curtailed plan — about $30 million less than originally envisioned — would lack sufficient vegetation along the banks of the river to deter geese from waddling in and leaving large amounts of excrement, which contains phosphorous and leads to algae blooms. The blooms reduce oxygen in the river and harm fish and other wildlife.

“We envisioned that you would be able to boat on this river,” Crockford said. “It seems foolhardy to not do this project as it was originally designed.”

Other longtime advocates of the project worry that insufficient dredging will eventually lead the Muddy to back up again from the accumulation of too much sediment, raising the risks of future flooding. Allowing the reeds, known as phragmites, to remain — they grow so densely that they can impede the flow of the river — is likely to lead to their rapid proliferation again, they add.

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“This is a very special part of a very special metropolitan park system,” said former governor Michael Dukakis, who lives near the river in Brookline and often walks beside it on his way to work at Northeastern.

Excavation was under way earlier this month in the Fenway.
Excavation was under way earlier this month in the Fenway.Wendy Maeda/Globe Staff

He said he has been lobbying the Obama administration and state officials to reconsider paying for the full project.

“I’m working my head off to get them to do the rest of it,” he said. “The Emerald Necklace is a real gem. How many cities have something like it?”

Army Corps officials said that no matter how much work they do, local officials are ultimately responsible for maintaining the river as free-flowing.

“We are doing what we can with the resources we have,” said Jennifer Flanagan, project manager for the Corps.

The project began in 2012 with the removal of about 200 trees throughout the area, including some that were a century old. By the time the first phase of the project finishes next spring, contractors will have replanted more than 200 maples, oaks, tupelos, and other trees, while adding 25,000 plants throughout the area.

In the coming months, there will be a final reconfiguration of the streets, including a realignment of traffic around the Landmark Center and the elimination of the so-called “jug handle” turnaround that feeds into Park Drive.

When all the work is completed toward the end of the decade, Flanagan said the new flood protections will safeguard the neighborhood from a storm similar to the one in 1996, which caused about $70 million in property damage.

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It will also restore about 40 acres of aquatic habitat and boost biodiversity, she said.

As cranes moved steel dikes and bulldozers pushed the earth near a new island that will soon be surrounded by the Muddy River, Margaret Dyson grew nostalgic.

The new parkland will be named after her former boss, Justine Mee Liff, who spent years fighting for the project as the city’s Parks and Recreation commissioner. She died in 2002.

Dyson called her a “visionary who imagined this restoration was possible.”

“She would be proud to see the river back where it belongs,” she said.

Brett Bourassa (left) and Jeff Rowett installed erosion fabric on wild flower seeds along the banks of the Muddy River.
Brett Bourassa (left) and Jeff Rowett installed erosion fabric on wild flower seeds along the banks of the Muddy River.Wendy Maeda/Globe Staff

David Abel can be reached at dabel@globe.com. Follow him on Twitter @davabel.