A U.S. Coast Guard helicopter responded to the beach at about 2:30 p.m. on reports of a person in the water off the Great Highway, between Moraga and Noriega streets.
Witnesses saw an inflatable boat carrying two people get flipped by a wave, and the two people went missing, fire Battalion Chief Lorrie Kalos said.
Rescuers were able to pull one person from the water at about 4 p.m.
The victim was hypothermic, and was unable to say who was in the boat or how many people were still in the water, Kalos said.
As of 4:30 p.m., crews were still searching for one other person.