Officers were called to the canal in Apperley Bridge earlier today when the man's body was discovered.
It led to speculation that there may be suspicious circumstances, with people on social media connecting it to a separate incident involving a report of a man with a gun in Silsden.
But a West Yorkshire Police spokesman said: "Police are aware of speculation on social media linking the discovery of a man's body in the canal at Apperley Bridge to a report of a man seen with a firearm in Silsden.
"These incidents are not being treated as linked and while the death of the man is still being investigated, it is not believed to be suspicious."
A man has now been arrested in relation to the incident in Silsden.