Emergency services were called to rapids on Sunday after the 50-year-old got into difficulty.
It has been reported that the man was sitting on rocks when he fell into the water.
Fellow members of Edinburgh Kayak Club went to his assistance after it was understood he entered the water at Clunie Dam to retrieve a paddle.
He was pulled from the water about an hour later and airlifted to Aberdeen Royal Infirmary.
A Police Scotland spokeswoman said he has since died.