The pilot was airlifted from the water, said Tanya Castaneda, a spokeswoman for the Port of San Diego. The pilot's condition was unknown.
KGTV-TV San Diego published a photograph of a downed aircraft in the bay's shallow waters.
Castaneda and Lee Swanson, a spokesman for the San Diego Fire-Rescue Department, said the afternoon incident occurred at the base in Coronado, near downtown San Diego.
They referred all questions to the military. Navy spokesman Kevin Dixon said authorities were collecting information and declined additional comment.