Renfrew area paramedics said the incident happened at about 3 p.m. in Palmer Rapids, Ont., about 200 kilometres west of Ottawa.
The man, in his 50s, was swimming at the time when a severe thunderstorm developed. He left the water and took shelter under a tree when he was struck, according to Michael Nolan, the chief of the County of Renfrew paramedic service.
He was treated by paramedics at the scene before being transported by air ambulance.
Much of eastern Ontario was under a severe thunderstorm warning at the time, with many regions also warned of the risk of tornadoes.