The man was pulled from the water by a lifeboat crew after getting in trouble around three miles north of Drumnadrochit at around 12:30pm on Saturday.
The kayaker, who was with another man, capsized after conditions became challenging during their journey from Fort Augustus towards Dochgarroch, near Inverness.
The second man alerted the coastguard, and a rescue operation involving the RNLI was launched.
The lifeboat crew found the man in the water holding on to his upturned kayak, but unable to either right himself or swim to the shore.
He was suffering from the effects of cold water immersion, and was taken to the lifeboat station where he received emergency care.
RNLI Loch Ness volunteer Vivian Bailey said: “The two kayakers were well prepared, well kitted out and, once the emergency occurred, made the critically important decision to quickly call for help.”