The man - identified only as Tony by South Australia Police - disappeared about 12.30pm on Saturday, sparking a three-day search effort.
According to police, he disappeared on Cordillo Downs Road, Innamincka, in the state's remote northeast.
"Despite efforts of emergency services and local volunteers, Tony was located deceased just after 10.30am," police said in a statement.
"There are no suspicious circumstances surrounding his death."
Throughout the search police worked closely with his family and keeping them informed of search activity and outcomes.
Search efforts involved aerial support, water operations officers, local police patrols and SES personnel.
"The Cooper Creek system remains in flood, with fast‑moving water, submerged hazards and restricted visibility," SA Police said.
Cooper Creek floodplain is part of one of the world's last major free-flowing desert river systems and regularly floods, according to the CSIRO.
It spans a large area of southwest Queensland and a smaller section of northeast South Australia.
"It is among one of the most complex floodplains in the world and is by far the most complex floodplain in Australia," the CSIRO states on its website.
Innamincka, where Tony disappeared, is more than 1000km north of Adelaide and about 40km from the Queensland border.
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