The emergency landing was reported around 4:20 p.m. Saturday, U-T San Diego reported.
The plane landed in the water just north of the San Diego-Coronado Bridge and were assisted by nearby boaters, Coast Guard officials said.
"Thanks to the quick actions of boaters who were in the area, the two men were only in the water for minutes after making the emergency landing," said Lt. j.g. Michael Haas, a spokesman for the Coast Guard. "Boaters took exactly the right actions, calling in the distress on Channel 16 and assisting the people in the water."
Divers have located the plane and are working with salvage companies to recover it.
What caused the plane to make an emergency landing was not reported.