A member of the public alerted the police after making the grim discovery on the banks of the River Dee just before 7am yesterday.
The area was cordoned off and a tent put up around the body as police made enquiries.
A Police Scotland spokesman said: "We can confirm that at 6.49am we attended at the south riverbank at the River Dee at Torry where a male was found deceased.
"Enquiries are at an early stage."
The body of the man was discovered just yards away from the river near where it connects with Aberdeen Harbour.
A spokeswoman for the Scottish Ambulance Service confirmed that paramedics had attended but were not required.
The man's identify has not been revealed and a post-mortem examination is due to take place.