The man was identified as 56-year-old David Junior Williams. Police say he likely drowned.
Mike Cherry, President of the Regional Land & Water Rescue Unit, said divers recovered William's body around 3:30 a.m.
The search for Williams began at 7:30 Saturday night after law enforcement was notified about a possible missing man in connection with a boating incident.
Wewahitchka Search & Rescue, C.A.R.E. Ambulance Service, the Troy Fire Department, officers from the Troy Police Department, Coroner Jerry Williams and Assistant Coroner Sandy Nasca responded to the scene.
Troy Police Chief Ennis said, "I would like to thank all the agencies and their representatives that assisted in the search for Mr. Williams over the last two days. I would also like to express to the Williams family that our thoughts and prayers are with them during this difficult time."