Officials said it had taken off from Mexico heading for Torrance went it went down.
The pilot reported problems to John Wayne Airport's tower before it went down.
"It was a distress call that they needed assistance and they needed a place to land," said Sgt. Steve Burdette of the Newport Beach Police Department. "We tried to help them by finding them a place to land but by that time unfortunately we lost communication and the last call was they were actually in the water."
Officials said the pilot tried to make an emergency landing on Newport Center Drive, less than a mile from where it crashed.
Rescue crews found the plane upside down in shallow water and pulled three men from the plane.
The names of the victims have not yet been released.
The tail number of the single-engine Beechcraft Musketeer comes back to a real estate agent from Palos Verdes Estates.
It is unclear whether he was on the plane.
The cause of the crash was being investigated by authorities.