Border Patrol spokesman Rodolfo Zuniga says one of the dead was found Tuesday night after the boat was discovered in Imperial Beach, a San Diego suburb north of the Mexican border.
Zuniga says he had no further details on that death.
Officials say the second death was a man found lying face down in a skiff packed with 15 suspected illegal immigrants that reached San Diego's Pacific Beach about 2 a.m. Wednesday.
Officials say 11 of them were treated for injuries and the other three are in custody.
Mexican smugglers have increasingly used boats to skirt border security and get illegal immigrants into California.