The 68 year-old man has been assessed by paramedics and treated for hypothermia.
He's been transported by the ACT Ambulance Service to The Canberra Hospital in a stable condition.
The alarm was raised by a passer by. It's believed he was in the water for 20 minutes by the time he was rescued by firefighters.
The ACT State Emergency Service are using a flood boat to retrieve the man's kayak.