A police spokesperson said they were called to reports of a man missing in the Koau branch of the Clutha River at about 5.30pm.
"A body has subsequently been retrieved from the river," the spokesperson said.
Earlier Fire and Emergency NZ crews had blocked Glasgow St about 50m from the river's edge, near the hangar at Balclutha Aerodrome.
An ambulance and a fire appliance were at the scene.
More than a dozen crew were seen working directly at the edge of the water.
It is the third water-related death in Otago this month after two men died in similar circumstances at Glenorchy.
The death will be referred to the coroner.