Werner Bachmayer (Vienna, 6 December 1960) is an Austrian sprint canoeist who competed in the early 1980s. He won a bronze medal in the K-2 1000 m event at the 1983 ICF Canoe Sprint World Championships in Tampere.
Bachmayer also competed in two Summer Olympics, earning his best finish of ninth in the K-2 500 m event at Los Angeles in 1984.