A federal judge on Monday denied Drakes Bay Oyster Co.'s bid to remain in business, upholding Interior Secretary Ken Salazar's decision that shuttered the commercial shellfish operation on the Marin County coast.

Judge Yvonne Gonzalez Rogers ruled that she lacked jurisdiction to review the decision by Salazar, who declined to renew a 40-year lease that gave oyster farm operator Kevin Lunny the right to operate in Drake's Estero.

The National Park Service, based on Salazar's decision, ordered Lunny to shut down the business by Feb. 28. The farm harvests 8 million oysters a year, worth about $1.5 million, from a 2,500-acre estuary designated as wilderness in the Point Reyes National Seashore.

Lunny filed suit contending that Salazar's order violated federal rules and was based on faulty science.

The judge, who heard oral arguments in her Oakland courtroom on Jan. 25, said that even if she had jurisdiction, Lunny's arguments were unlikely to prevail.

Wilderness advocates who sought removal of the oyster farm hailed the decision and said they hoped it will bring the divisive issue to an end.

"It's time that we all move on," said Neal Desai, pacific region associate director of the National Parks Conservation Association. "This decision was very clear and straightforward."

Desai said the decision "affirms that our national parks will be safe from privatization schemes" and that national seashore land owned by taxpayers "will now be protected as planned after 40 years of waiting."

Amy Trainer, executive director of the Environmental Action Committee of West Marin, said the court "rightly decided that Secretary Salazar had full discretion to let the oyster operation permit expire on its own terms and honor the 1976 wilderness designation for Drakes Estero."

The prolonged dispute pitted supporters of West Marin agriculture, who fear the loss of permits for onshore ranches in the national seashore, versus wilderness advocates who want all human activity removed from the estero.

Nancy Lunny deferred comment to representatives of Cause of Action, the Washington, D.C.-based nonprofit watchdog that represented the oyster farm for no charge. Amber Abbasi, an attorney for the group, said in an e-mail that she was disappointed with the ruling.

"Without this injunction, not only will a small business close, but families will be forced out of their homes, and the community will lose a sustainable farming resource," Abbasi said.

The Lunnys are "weighing their options for next steps and will make their decision known in the coming days," Abbasi said.

The oyster company was seeking a court order postponing the closure until the legal case was resolved.

Among its arguments, the company cited the prospect of immediate and irreparable financial harm to the operation and its 31 full-time employees.

The judge acknowledged that the company and its workers "will suffer significant costs," including loss of jobs.

"The close of any business frequently brings hardship," Rogers said in a 31-page decision.

She also noted the Lunnys knew, upon buying the oyster farm in 2004, that the Park Service did not intend to renew their permit. The family's expressed hope for an extension was not "based upon any assurances by the decisionmakers themselves," the judge wrote.

Rogers also dismissed the Lunnys' contention that Salazar's decision was based on bad science, an issue that inflamed the yearslong debate over the oyster company's future.

"At best, the record before the court is mixed with competing expert declarations . . . and cannot be resolved at this stage," the judge said.

In summary, she said the oyster farm "cannot establish that the Secretary's refusal to issue the (permit) was arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law such that they would ultimately be successful on the merits of their claim."

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