Chalong Police investigator Patiwat Yodkwan said that Georg Erwin Bach, a 64-year-old Phuket resident, was attempting to take off when the machine suffered engine failure.
Initial reports said that the aircraft exploded when it was about 500 metres up in the air. Staff of the nearby resort, formerly the Evason, dived into the water to try to help.
Mr Bach was pulled from the water, but he had already drowned after being trapped in the wreckage by his safety harness. His body was taken to Vachira Phuket Hospital.
Mr Bach was seen yesterday was seen taking off but then landing again abruptly, apparently with some sort of engine trouble.
The flying machine is basically a rigid inflatable boat with a microlight wing attached.
Rawai Mayor Aroon Solos said, "There are not many flying boats around here. They are expensive, so the people who fly them have to be very rich."
Additional reporting Eakkapop Thongtub.