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Drakes Bay Oyster Co. did not remove all the oysters and clams from the water at Point Reyes National Seashore prior to vacating the government-owned property last week, National Park Service officials said this week in a finding confirmed by underwater videos shot for The Press Democrat.

Ben Becker, the national seashore’s marine ecologist, said he saw several hundred oyster strings on two wooden oyster growing racks during a snorkeling survey conducted from a 12-foot outboard motor boat this week, when the videos were taken.

Park service officials found oysters and clams in the water during a previous assessment by boat on the estero on Jan. 1, the day after the oyster company vacated its five-acre site at the north end of the 2,500-acre estero, an ocean water body rich in plant and animal life.

Oysters were found in growing bags resting on sandbars and on metal strings attached to some of the 95 growing racks planted in the shallow estuary’s sandy bottom.

“We are in the process of assessing how much (shellfish remains in the water),” said Melanie Gunn, outreach coordinator at the national seashore in west Marin County.

Park service personnel have surveyed “the entire growing area,” including the racks and sandbars, she said.

The park service is also investigating the presence of chunks of solid foam — the remains of a company-owned barge — on the shoreline near the abandoned oyster farm, Gunn said.

The oyster company, owned by the Lunny family, complied with a federal court-approved settlement agreement to leave the estero at midnight Dec. 31 but did not fulfill all the terms of the agreement, Gunn said.

Co-owner Kevin Lunny said his crews worked for four months to remove all the shellfish.

“We thought we had them all,” he said. “We took that agreement very seriously and did everything in our power to comply.”

Responding to the park service’s comments, Lunny said “it sounds like we may have missed a few,” noting that the growing racks are spread over about half of the estero.

“We didn’t want this to happen,” he said. “This is not the Lunny family leaving garbage behind and trying to duck it.” Lunny said he is willing to talk to the park service about what should be done now, but the agency has not contacted him.

In an effort to clear the estero of shellfish, Lunny said he disposed of 5 million oysters and 1 million clams. He was allowed to sell shellfish of marketable size during the cleanup period.

Gunn said the company was obliged to remove all shellfish in bags and on racks under the agreement it signed in October. No penalty for failure to fulfill that requirement was established, and the company’s cleanup obligations ended on Dec. 31, she said.

“I don’t know what steps we’re going to take,” Gunn said, noting that the park service is now undertaking a “full assessment” of the estero.

Drakes Bay, which acquired the oyster farm in 2004, had harvested $1.5 million worth of oysters a year from the waterway’s clear, cold waters under a government permit that expired in 2012.

The settlement agreement reached between the company and the park service ended Lunny’s two-year legal battle over the loss of its permit, which former Interior Secretary Ken Salazar declined to renew.

Neal Desai, director of field operations for the National Parks Conservation Association’s Pacific Region, said he was dismayed by the condition of the estero, which will now achieve wilderness status after 80 years of commercial oyster production.

“This place is trashed,” he said. “The oyster company had a responsibility not only to the park service but to the American public to make sure it was cleaned up and they failed to do that.”

Desai said it was “unacceptable” for the company to leave behind what he described as “non-native, invasive” aquaculture species, calling it evidence of the farm’s poor environmental stewardship.

Effective Jan. 1, the park service became responsible for the removal of all property remaining on land and in the water, according to the settlement agreement.

The 95 growing racks in the estero are each 300 feet long by 12 feet wide on average, collectively weighing about 375 tons and stretching for five miles.

Demolition of the oyster farm’s onshore structures will start and likely be completed next week, Gunn said. Five dwelling units occupied by former oyster company workers will remain until the end of March.

On Wednesday, an unseasonably warm wind rippled the water and blew through the three weatherbeaten buildings left behind by the oyster company at the northern tip of Schooner Bay, one of the estero’s five fingers. The oyster sales shack, once a busy visitor destination, was stripped of its sign and doors, with a few pieces of furniture, shelves and a white board listing the wholesale oyster delivery schedule inside.

In the non-chilled refrigerator room were cans of tomato juice, bottles of bloody mary seasoning, a jug of Worcestershire sauce, lemons and a magnum bottle of Cooks Brut champagne.

The wooden dock and oyster processing area was littered with hoses, plastic crates, rubber gloves, tools and cans of trash. Small chunks of brownish foam lay on one part of the beach, amid oyster shells and pieces of broken French tubes used in oyster cultivation.

Richard James, an Inverness activist, was the first to report foam in the estero in his blog following his own kayak trip in the estero on Jan. 1.

“I was shocked,” said James, who calls himself the Coastodian. “The day after the last day (of the oyster farm’s operation) here’s this giant mess.”

James said he found large and small foam chunks floating at the tip of Schooner Bay, where both the oyster farm and a public access point to the estero are located. Paddling back toward the access point against an outgoing tide, James said “thousands of chunks” of foam were sweeping past him toward the Pacific Ocean.

Gunn said Tuesday she had seen photographs of floating foam on James’ website and there “seems to be quite a bit of foam on the shores now.”

The oyster company’s flat wooden barges, used to haul bags and strings of oysters to the farm, were buoyed by large pieces of foam, she said.

The dock and all the buildings at the five-acre oyster farm site are government property, but the barges were the company’s “personal property,” she said. The company had the option to remove the barges by Dec. 31 but was not obliged to do so, Gunn said.

Lunny said the last of four aging barges broke apart while his workers were dragging it up the beach at low tide on Dec. 31, and his crew picked up broken pieces of foam in the dark. “It was unavoidable and we took care of it,” he said, acknowledging that workers may not have collected “every single piece.”

The incident was reported to government attorneys and to the Point Reyes Seashore superintendent’s office, Lunny said.

The company used four barges that the oyster farm’s previous owner had floated down from Washington state in the 1950s, he said.

The agreement also required the oyster company to file monthly reports on its progress in removing shellfish from the estero. Initial reports said the company had removed nearly 500,000 oysters in September and October.

No reports for November and December have been filed and the park service is requesting them, Gunn said. Lunny said the reports are “forthcoming.”

Public collection of shellfish from the estero is banned because of concerns raised by state public health officials of potential poisoning from toxins that occur in the waterway, Gunn said.

Any mollusks that remain in the estero following the oyster company’s departure would be “an attractive target to poachers” and could be a health threat if harvested and consumed during “harmful algal bloom events,” a state public health official said in a letter to the park service in July.

While it was harvesting oysters, the company provided weekly samples to the state Department of Public Health for testing, the letter said. The estero is a “high-risk area” for toxins that cause paralytic shellfish poisoning, it said.

The remaining shellfish will be removed from the water “on an emergency basis,” Gunn said.

Becker, the national seashore’s chief scientist, said he’s waiting to see how the estero’s vast eelgrass beds grow back after the oysters racks are removed. The estero is home to a harbor seal colony, leopard sharks, bat rays, crabs and a wealth of birds and fish.

A popular kayaking spot, it will continue to be open to nonmotorized boats, except during seal pupping season from March through June.

“It’s a beautiful place,” Becker said.

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

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Editor’s note: This story has been altered to reflect the following correction:

The name of Richard James, an Inverness activist, was misspelled in a story about the former oyster operation in Point Reyes National Seashore.