Police officers were called to the incident at around 4.40pm on Saturday in the area of Catterline Bay near Stonehaven.
The force said in a statement that the 61-year-old died after a small fishing vessel capsized.
Two other men on board the boat, a 67-year-old and a 58-year-old, were taken by ambulance to Aberdeen Royal Infirmary.
Police said there are no suspicious circumstances surrounding the man's death.
His family have been notified and a report will be submitted to the Procurator Fiscal.