Emergency services were called at 14:50 BST on Tuesday to a river at Aberglaslyn, near Beddgelert.
Formal identification is expected to take place later today. Specialist police are supporting the man's family.
Ch Insp Mark Armstrong said: "Our sympathies go out to the family and friends of the person involved."
He said the operation to recover the body had been complex and involved police, North Wales Fire and Rescue Service, Aberglaslyn and Ogwen mountain rescue teams and the regional police underwater search teams.
A body has been recovered in the search for a canoeist who got into difficulty in Snowdonia, police have said.