The man's family reported him missing Friday when he did not return from a fishing outing, Durgerian said. The man is approximately 39 years old, he said.
Visitors in the area of Battery Rathbone-McIndoe found the body on the beach at about 3:30 p.m., Durgerian said.
They notified National Park Service rangers, and the California Highway Patrol used a helicopter to recover the body, Durgerian said.
The high surf prevented crews from recovering the body by boat, Durgerian said.
Marin County sheriff's Sgt. Keith Boyd said the man's name won't be released until an autopsy today determines the cause of death.
"There is no reason to suspect foul play," Durgerian said.
Guns at the historic battery were used during World Way II to defend the minefields outside the Golden Gate from minesweepers, according to the California State Military Museum. The battery was deactivated in 1945.