The teenager is believed to have fallen into the Luggie Water where he was later found.
Emergency services were quickly on the scene near to Old Duntiblae Road in the town and the young man was removed form the water and then taken by ambulance to the Queen Elizabeth Hospital in Glasgow.
A spokesperson for Police Scotland said: “Around 7pm on Saturday, March 2 police were called to a report of a person within the water near to Old Duntiblae Road, Kirkintilloch.
“Emergency services attended and a 16-year-old male youth was removed from the water and taken to the Queen Elizabeth University Hospital where he was pronounced dead.
“A post mortem examination will be carried out in due course to establish the exact cause of death, which officers are currently treating as unexplained.
“His family have been made aware and a report will be submitted to the Procurator Fiscal.”