Thomas McGowan, 63, was taken to the Southern General Hospital in Glasgow by air ambulance after the incident on the Isle of Bute on Saturday but he died yesterday.
A 52-year-old man, who was also on board the small aircraft, was airlifted to the Royal Alexandra Hospital in Paisley and remains in a critical condition, police said.
Officers 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.
They have appealed for any witnesses, and are also keen to get any video or mobile phone footage people may have of the aircraft.
Mr McGowan's family have been informed of his death and a report is to be sent to the procurator fiscal.
Anyone with information is asked to contact Police Scotland on 101.