Boaters rescued the pilot from the bay that separates the Navy base in Coronado from downtown San Diego, the Navy said.
The pilot was taken by helicopter to University of California, San Diego, Medical Center for evaluation and was released.
The pilot was training for aircraft-landing qualifications in a T-45C Goshawk when the crash occurred. Lt. Reagan Lauritzen, a Navy spokeswoman, said there was no one else aboard.
The downed aircraft could be seen in the bay's shallow water, barely offshore from the base. The Navy was working to lift the jet out of the water.
The cause was under investigation.
The T-45C Goshawk is a tandem-seat jet used to train Navy and Marine Corps pilots. The downed aircraft was assigned to Training Squadron Nine, stationed in Meridian, Mississippi.