The canoeist was pulled out and taken to hospital by air ambulance.
A spokesman for the Great North Air Ambulance said: ""A canoeist, a man in his 30s, was trapped in the river. After a search the man was located and pulled from the water.
"We took a doctor and paramedic to the scene who worked on the patient at the scene and throughout the flight to James Cook University Hospital (in Middlesbrough).
"This was a large-scale rescue effort involving police, fire, RAF and Swaledale Mountain Rescue Team.
"Sadly, despite everyone's best efforts, the man was later pronounced dead. Our thoughts are with his family and friends."