Ricky Flores, 42, was thrown into the water, along with two other men, on March 21 when their boat overturned in the Wild Sheeps rapids about six miles north of Hells Canyon Dam.
Charles Gissel of Ontario, Ore., and Eric Meyerhoffer of Payette were able to get to shore, but Flores wasn't found.
Wednesday, the sheriff's office says that someone spotted a body in the river about 13 miles downstream from the Hells Canyon Dam boat launch.
Officials say identification found on the remains was that of Flores and that they believe it is the missing man.
The remains will now be investigated by the Baker County Medical Examiner.