Moelfre inshore lifeboat launched at about 11:00 BST, along with the local coastguard team and rescue helicopter from Caernarfon.
The lifeboat crew found the man in his forties clinging to his fishing kayak, having struggled to climb back on.
He showed signs of immersion and was transferred to Ysbyty Gwynedd in Bangor.
The man, who was wearing all the correct safety equipment, estimated he had been in the water for more than 15 minutes.
Lifeboat helm Alan Owen said the man was "coughing heavily" by the time they got him to the beach "which is a clear sign of salt water ingestion".
Mr Owen praised the multi-agency response, which he said resulted in a "quick and efficient rescue".
An RNLI crew came to the rescue of a capsized kayaker off Anglesey on Friday.