Authorities discovered the body of 53-year-old Roger Christiansen of Marin County in the water near Fort Funston, which is about three miles south of Ocean Beach.
Authorities did not determine a cause of death.
Christiansen disappeared April 9 after the boat he and a companion were in began taking on water. The two were apparently headed to Pacifica to retrieve a lost boat.
Christiansen's companion was rescued by the U.S. Coast Guard.
However, the search for Christiansen was called off about nine hours after the Coast Guard determined he was not likely to have survived that long in the cold waters.
The Associated Press contributed to this report.