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The steel arm of an excavator positioned on a hulking barge pulled dark chunks of debris from the windswept waters of a marine wilderness Wednesday in the Point Reyes National Seashore.

Soggy refuse — oyster shells, pressure-treated lumber and plastic tubes — was dropped into a pair of dumpsters aboard the vessel for unloading on a beach at the north end of Drakes Estero and ultimately transport to a landfill.

The work under cloudy skies came during the final weeks of a $4.5 million restoration project eradicating nearly all remnants of eight decades of commercial oyster cultivation in the biologically rich 2,500-acre Pacific Ocean estuary, a popular kayaking spot known for its harbor seal colony and the rich life in its waters, including leopard sharks and bat rays.

On this day, the excavator operator was taking pains to scrape only a few inches into the estero’s muddy bottom, retrieving refuse while minimizing impact on the fragile ecosystem.

“These guys are really careful,” said Ben Becker, the seashore’s marine biologist, manning a 16-foot steel workboat near the barge.

Workers have also given a wide berth to the seals, seen resting on a distant sandbar during their pupping season.

Becker and two assistants were on hand to document the impact through a precise series of underwater photographs taken before and now after the excavator had cleaned the locations where 95 wooden oyster racks — stretching a cumulative 5 miles — were once scattered around the shallow estuary, which averages 4 to 5 feet deep.

Divers had moved in behind the excavator, feeling by hand for chunks of debris buried in the muck, including pieces of racks that collapsed decades ago.

The cleanup, expected to be complete in early May, has removed more than 500 tons of lumber and more than 1,200 tons of oyster shells and plastic tubes that were used in cultivating the prized bivalves.

Taxpayers funded $2.5 million of the Park Service restoration project and the National Park Foundation, a charitable, nonprofit partner of the federal agency, contributed $2 million.

Cicely Muldoon, the seashore’s superintendent, said the money was well spent.

“It’s a great success story,” she said, calling the restoration “a gift to our visitors today and to future generations.”

The seashore, established in 1962, draws 2.5 million visitors a year to its 71,000 acres of forests, beaches, bluffs, trails and backcountry campsites close to the urban San Francisco Bay Area.

The estero officially became wilderness following the government’s eviction of the Drakes Bay Oyster Co.at the end of 2014, culminating a political and legal battle that drew national attention and sharply divided the west Marin community. Oyster farm supporters, including many in local agriculture and sustainable food circles, remain dismayed by the operation’s ouster.

On the other side, wilderness and park advocates have welcomed the estero’s cleanup.

“Americans can now enjoy a unique resource they own, unlike any other on the West Coast, where the sounds and sights of nature — not motorboats and plastic pollution — greet visitors who hike or kayak this wildlife paradise,” said Neal Desai of the National Parks Conservation Association, which pressed for removal of the oyster farm.

Out on the choppy, wind-ruffled water Wednesday, Taylor Ellis, a Park Service wildlife technician, donned a dive suit and manned a GoPro camera rig to record the effectiveness of the cleanup and its impact on eelgrass, a marine plant with long ribbon-like leaves.

Sarah Codde, a marine ecologist, assisted in setting 50-meter lengths of yellow rope between plastic pipes jammed into the mud to define Ellis’ snorkeling routes over the places where racks once rested.

“So far it looks like the impacts have been far less than we anticipated,” Becker said, despite the fact there turned out to be “far more debris out here than we thought.”

The National Marine Fisheries Service and California Coastal Commission are closely monitoring the Park Service’s reports on the estero’s eelgrass, a cornerstone of the marine environment that is diminishing worldwide.

One of the major reasons for the cleanup, Becker said, is the hope that eelgrass will grow back into the largely denuded areas under the oyster racks.

Removing debris is also intended to curb the presence of an invasive species of sea squirt, commonly known as “marine vomit” for its unappealing gelatinous mass.

But it was fundamentally a matter of good housekeeping.

“If this were on land, would you leave a big pile of trash here?” Becker said.

You can reach Staff Writer Guy Kovner at 707-521-5457 or guy.kovner@pressdemocrat.com. On Twitter @guykovner.