A dog walker spotted the body in Vernatt's Drain, near the Pinchbeck Road bridge in Spalding, on Sunday.
Police recovered the body from the water after being alerted shortly after 14:00 GMT.
Officers had been initially treating the death as unexplained, but said they were now classing it as not suspicious.
The man's details are yet to be released.
The death of a man found in a Lincolnshire waterway is not being treated as suspicious, police have said.