Timothy Cunningham left work at the Centers for Disease Control and Prevention (CDC) in Atlanta on 12 February, saying he was feeling unwell.
Police say they do not suspect any foul play, but have not ruled it out.
The Harvard graduate had worked on tackling the Ebola and Zika outbreaks before his death.
His body was found late on Tuesday by a group of fishermen.
According to the Atlanta Business Chronicle, Cunningham, who was known to collect rocks, was found with crystals in his pocket and wearing running shoes.
His death has been classified as a drowning.
Mr Cunningham, who was an epidemiologist in the CDC’s chronic disease department, lived with his dog.
Timothy was a Harvard graduate and worked on tackling the Ebola and Zika outbreaks before his death. Investigators found Timothy Cunningham’s keys, phone, wallet with identification and credit cards safely locked in his home back in February when he went missing. Police are saying no foul play, his death was classified as a drowning.