Drakes Bay Oyster Company must evacuate Drakes Estero and harvest its final bivalves by midnight on Dec. 31, 2014, according to a settlement reached last Tuesday between the oyster farm and the federal government and approved by a federal court this week.

Though the end has never been more clearly in sight for Drakes Bay, farm owner Kevin Lunny and his family will soon have a new oyster business in Inverness that will employ many of their longstanding workers: Drakes Oyster House, which will take over the years-vacant restaurant space at the Tomales Bay Resort. 

Mr. Lunny, citing his passion for shellfish aquaculture, is also investigating possible new locations for another oyster farm on the Pacific Coast.

The new restaurant, which could open as early as next month with a limited menu and hours for the winter, will be “on the casual side,” Mr. Lunny said, starting out with oysters, chowder, soups, fish and chips and burgers. It will feature local ingredients, including the organic beef and vegetables grown on the family’s G Ranch. Customers will also be able to buy bags of oysters to go.

“We fell in love with connecting people to their food. That’s what was so special about the oyster farm: the 50,000 [annual] visitors that came with their families and learned where their food came from,” Mr. Lunny said. Though he had been unsure about announcing the new venture this week, he said he didn’t want the news of the oyster farm’s final closure to “look like a eulogy.”

Mr. Lunny said he is setting up the restaurant as a benefit corporation. Though he is still hammering out the details, he plans to create an educational component—perhaps farm tours or boat tours of Tomales Bay oyster growers. The benefit might also include providing space for nonprofits or offering the kitchen to artisan food producers. He and Jeff Harriman, who owns the resort, are currently interviewing chefs.

In a separate venture, Mr. Lunny is also planning to distribute oysters to Bay Area restaurants. Though has not yet determined whose oysters he will sell and serve at the restaurant and distribute more widely, he said they could come from as near as Tomales Bay and as far away as Mexico. “Baja California grows fantastic oysters,” he noted. 

The settlement with the federal government marks the end of Drakes Bay’s nearly two-year legal battle with the Department of the Interior that never went beyond an initial request for an injunction. Drakes Bay filed a lawsuit after then-Secretary Ken Salazar ordered the company to shut down in November 2012 and opened the door for the estero’s conversion to a marine wilderness, though the lengthy and fiery controversy over the farm’s fate kicked off in earnest years earlier, in 2007. 

In its suit, the farm alleged that the federal government illegally turned down its request for a permit renewal and violated the National Environmental Policy Act and other laws. But both a district court and the Ninth Circuit Court of Appeals sided with the government, and the Supreme Court declined to hear the case this summer. The farm ended retail operations and closed its cannery—the last remaining cannery in the state—on July 31, but it has continued to harvest and sell oysters wholesale to restaurants and markets. The farm will harvest what it can in the next few months, although millions of pounds of oysters that won’t reach market size this year will have to be thrown away.

As part of the settlement, Drakes Bay agreed to bring no more lawsuits against the government. The National Park Service took on the task of removing the oyster racks at its own expense, though in the past it said that would be the oyster farm’s responsibility. It, too, agreed to not pursue any administrative claims against the farm, such as for trespassing. The seashore can start cleanup efforts and remove property not connected to shellfish operations immediately, “advancing the Park Service’s goal of expeditiously transitioning Drakes Estero to management as a marine wilderness,” the settlement says.

According to the environmental impact statement on Drakes Estero, finalized in 2012, the park will remove the main dock, a work platform, a stringing shed and the southern pier. The fate of other structures is yet to be determined, said Melanie Gunn, a spokesperson for the seashore, as the court only approved the settlement Wednesday morning and the park is still working out the next steps.

The E.I.S. said removal operations would cause some minor adverse impacts to fish, including coho salmon and steelhead trout, as well as birds, seals and eelgrass. In the long term, the evacuation of the farm would benefit the natural environment, including providing up to 88 more acres of intertidal bird habitat, it stated. (Drakes Bay disputed many of the conclusions and evidence contained in the impact statement.)

The statement also said that, both after the farm’s closure and under one of the alternatives that would have allowed the farm to remain, the seashore would hire two part-time, seasonal workers to “assess and monitor invasive species and other resources of concern” in Drakes Estero. 

Ms. Gunn said she was unsure what the seashore’s plans were for hiring people to monitor invasive species, or how much the removal project would cost. “We will [now] begin reconnaissance: how to go about it, how big is the project, all those different things,” Ms. Gunn said. 

She said the park is reaching out to agencies like the Army Corps of Engineers and the California Coastal Commission to determine just how to remove the five miles of oyster racks. The park will likely contract out that work, which can theoretically begin as soon as the racks are emptied and as long as their removal doesn’t interfere with the remaining harvest. 

The settlement requires Mr. Lunny to remove 50 percent of his shellfish from the racks by the end of October and 75 percent by the end of November.

The park says it will provide relocation benefits like rental assistance to “qualified employees” living in the five units of worker housing on the farm, and allow them to live there for at least the first three months of 2015.