Members of the public pulled the man to safety after the incident this morning in the village of Pennan.
Emergency services were called just before 11am today, police said.
He was flown to Aberdeen Royal Infirmary by RAF Rescue Helicopter 137 from Lossiemouth.
It is thought he may have been trying to turn the scooter when it went into the water.
The Scottish Ambulance Service said that the man suffered a head injury but there was no further information about his condition.