The migrants were dropped offshore by a boat believed to have returned to Mexico, Encinitas Fire Chief Mike Stein said.
Emergency crews responded to calls of people yelling in the water early Friday morning, Stein said.
Three people were pulled from the ocean and another 10 reached the shore on their own, according to Stein.
The 13 people were taken to local hospitals for treatment of mild hypothermia, deputy fire chief Robert Ford said.
Divers were searching for three who were still unaccounted for, authorities said.
“This is a ‘dump and run’ where the panga doesn’t actually make it to shore,” Stein said. “The boat drops people off to swim, then returns to Mexico.”
A panga is a boat often used for working off the coast of Mexico or Central America, according to the US Coast Guard. The engine-powered vessels are typically 25 to 45 feet long.
Authorities were searching for the boat and two operators, according to US Border Patrol Agent Kurtis Kantura.
Kantura said panga boats are dangerous because they lack communication devices.
“They care little for human life and will do anything they can to make a dollar,” he said of the boat operators.
The nationalities of the people rescued have not been determined, Kantura said.