The incident unfolded Sunday night, according to the Los Angeles County Sheriff's Department. Deputies found the toddler on the vessel which was in a slip.
Divers took to the water searching for the child's parent or guardian, believing an adult may have fallen off the boat, leaving the child alone.
A few hours later, the child's mother turned up with a male companion. Both of them were arrested for child endangerment.
The child was not harmed and is now safe. Additional details were not available.