The oyster farm battle even divided the state's two powerful senators. Sen. Dianne Feinstein, D-Calif., criticized Salazar's decision as based on flawed science, while Sen. Barbara Boxer issued support.
Lunny's lawyers said they intend to ask a judge on Friday to issue an injunction that would block the oyster farm's eviction while the lawsuit makes its way through the courts.
The oyster farm was given 90 days to cease operations after its lease expired Nov. 30. The company can continue harvesting during that time.
Lunny said there are millions of young oysters in the water representing millions of dollars in lost revenue if he is forced to tear them out in 90 days.
The farm produced about 40 percent of California's commercial oysters.
"Oysters used for food in (San Francisco) Bay Area will have to be imported now," Lunny said.
Environmentalists who opposed extending the oyster farm's lease said the process was fair and thorough, and that the lawsuit is sour grapes.
"Taxpayers bought this property and it was long-planned to be our first marine wilderness on the West Coast," Neal Desai, associate director of the National Parks Conservation Association, said.
"This lawsuit is clearly an attempt to privatize (Drakes) Estero and rob the public of this great gift the secretary has given all Americans. The company should really move on."