The accident happened shortly after midnight, according to Imperial Beach Fire Chief John French, who told local outlet Sideo TV that one body was recovered near the site of the capsizing, while three were located near the Imperial Beach Pier.
Five survivors were rescued and transported to a hospital, and the US Coast Guard continued search operations into early Saturday, French said, Xinhua reported.
The Times of San Diego reported that it remained unclear whether the vessel was involved in an attempt to smuggle migrants into the United States.
Conditions were rough at the time of the incident, as moderate-to-heavy rain began sweeping across San Diego County. Southern California was hit on Saturday by the most intense phase of a Pacific storm fueled by a plume of subtropical moisture.