Drake’s Bay Oyster Company appealed on Wednesday a U.S. District Court ruling that the company could not remain in operation while it wages a lawsuit against the Obama administration.

U.S. District Judge Yvonne Gonzalez Rogers ruled on Monday that it was beyond the court’s jurisdiction to grant Kevin Lunny’s request for a court order invalidating Secretary of the Interior Ken Salazar’s decision to terminate oyster farming in Drakes Estero.

Judge Gonzalez Rogers’ 31-page ruling, which was denounced by Lunny’s attorneys as based on “errors of law” and “clearly erroneous findings of fact,” found that even if the court had the authority to consider the request—and even though the closing of the farm was likely to cause the Lunnys’ business “irreparable harm”—their legal claims were without merit and unlikely to succeed in court.

“Discretion, by its very nature, affords the Secretary myriad outcomes. Plaintiffs have failed to provide any evidence of Congressional intent to the contrary,” Judge Gonzalez Rogers wrote. She said that the government, defendants in this lawsuit, did not deceive Lunny or suggest that any new special use permits would be issued after they purchased the property or after the lease expired last year. “To the contrary, Defendants acted affirmatively to warn the Lunnys at the outset of their intention to allow the Reservation to lapse without a [new special use permit] and reiterated this position over time. The Lunnys’ refusal to hear the message weighs against them.”

The appeal marks the latest salvo by the Lunny family and their allies in what has become a legal battle between those who want to keep the oyster farming and cannery business alive and those who wish to see the Point Reyes National Seashore estuary restored to wilderness.

“If she made a decision and it looked like it was properly made on the law and she did a correct analysis and we didn’t think we’d have a chance, we wouldn’t make an appeal,” Mr. Lunny said Wednesday. He described his mood as disappointed by the ruling, but encouraged that the basis of the ruling was wrong. “We’re still here. We plan to be here. The community has not given up and this is a community resource. So we’re going to stick this out because it’s the right thing to do.”

Mr. Lunny noted that his staff is anxious about the details of litigation as the February 28 closure date for the oyster farm approaches.

Neal Desai, of the National Parks Conservation Association, told the San Francisco Chronicle that the ruling “affirms that our national parks will be safe from privatization schemes, and that special places like Drakes Estero will rise above attempts to hijack Americans’ wilderness.”

In a separate ruling on Monday, Judge Gonzalez Rogers denied a request by Mr. Desai’s group and three other environmental nonprofits to intervene in the lawsuit. The judge said the groups—including the Environmental Action Committee of West Marin, Save Our Seashore and the National Resources Defense Council—were likely to be adequately represented by the federal government.

The groups may still be allowed to submit briefs in cases “where their unique perspective would contribute productively to the
discussion.”

A large portion of the decision to let Drake’s Bay Oyster Company close hinged on an amendment, written by Senator Dianne Feinstein, to a 2009 appropriations bill that was intended to put the extension of the Lunnys’ lease on solid legal footing. Instead, Judge Gonzalez Rogers agreed with lawyers for the federal government, who argued that the amendment, Section 124, gave courts “no meaningful standard” with which to review a decision that was left to Salazar’s
discretion.

The judge added that Mr. Lunny strains “credulity” in calling Salazar’s use of discretion “arbitrary and capricious” when, according to the judge, he wrote two letters to Mr. Salazar that show he understood the secretary had exactly that authority.

“Plaintiffs claimed at oral argument that they had ‘every reason to hope’ for a [new permit] but the record does not reflect that their hope was based upon any assurances by the decision-makers themselves.”

Judge Gonzalez Rogers said the court had little basis for evaluating claims of scientific misconduct,  political overreach or environmental impact.

Mr. Lunny said his appeal, to the United States Court of Appeals for the Ninth Circuit, will focus on the judge’s interpretation of Section 124. He deferred to his lawyers at Cause of Action, a Washington-based nonprofit government watchdog group, on specific legal questions. They did not respond to a request for comment Wednesday evening.