The 63-year-old was taken to the Southern General Hospital in Glasgow by air ambulance after the crash on the Isle of Bute yesterday.
He died this morning.
A 52-year-old man, who was also on board, was airlifted to the Royal Alexandra Hospital in Paisley and remains in a critical condition.
Police Scotland are working with the Air Accidents Investigation Branch to investigate the crash, which happened at around 3.45pm between the Kilchattan Bay and Kingarth areas of the island.
Officers have appealed for witnesses, and would like to obtain any video or mobile phone footage.
The man's relatives have been informed of his death and a report will be submitted to the procurator fiscal.
Anyone with information is asked to contact Police Scotland on 101.