A rescue operation was launched late on Tuesday evening when a member of the public saw the kayak with no-one in it off Fidden campsite on the Isle of Mull.
Coastguard teams and the Tobermory RNLI all-weather lifeboat carried out searches but found no trace of anyone.
On Wednesday morning, the Stornoway coastguard helicopter and the Oban RNLI lifeboat were also involved in the search.
The body of a man was recovered from the water at around 11.52am on Wednesday.
Police said investigations are under way to identify him.
A police spokesman said: "The body of a man was recovered from the water following a search by the coastguard rescue helicopter and Oban RNLI lifeboat.
"Police inquiries are ongoing to identify the man and trace his family."