Authorities received a call early Saturday from someone who heard voices yelling for help in foggy Monterey Bay, said Capt. Doug McCoun of the North County Fire District.
Authorities rescued two of the men, Danny Regalado and Leonel Paredes, and took them to a hospital, where they were treated for hypothermia.
Rescue efforts were called off at 11:30 a.m. after authorities failed to find the missing man, Jose Luis Valdez, who is believed dead. Teams planned to conduct an aerial search when the fog lifted.
Valdez was not wearing a lifejacket, authorities said.
Rescuers retrieved the 18-foot-long motorboat, which sank about 100 yards offshore, McCoun said.
Authorities still do not know what caused the accident. Although visibility was poor, the seas were calm, McCoun said.
Monterey is about 90 miles south of San Francisco.