The city's missing persons squad discovered the body of Afonso Freire de Novais Santos Tiago near the Schilling Bridge – not far from several popular Berlin clubs – using a boat with sonar equipment.
Friends and relatives had started an unprecedented search for the man after he disappearing following a night out on January 10.
Police said they currently had no evidence of foul play in the man's death.
Only on Tuesday, a Colombian man missing since mid-February was found dead in another arm of the Spree. The captain of dredging boat plying the Landwehr canal discovered his body in the Kreuzberg district.
The authorities expect an autopsy will determine the cause of the Colombian's death in the coming days.