The single-engine plane had left Scott Lake, Sask., on Aug. 23 and was reported overdue the next day.
The partially submerged aircraft was later spotted in Ivanhoe Lake, but there was no trace of the pilot, who was the only person aboard.
The plane belongs to Transwest Air, a company based in Prince Albert.
Mounties said the pilot's remains will be brought to Stony Rapids, Sask., for examination by the coroner.
No information on the pilot has been released.