He was located a short distance from where the kayak was reportedly seen and was motionless in the water.
"Eagle liaised with Fire Rescue Service at Auckland International Airport and requested their staff and hovercraft to assist," police said.
"From the air, Eagle staff communicated by using hand signals with the man, at which point he indicated that he was not okay."
An Eagle crew member was tasked to assist the man stuck in the water and stayed with him providing flotation and reassurance until the hovercraft arrived.
A St John spokesperson said an ambulance treated a patient in Titirangi at 1.51pm and transported him to Waitakere Hospital in a serious condition.
Police report the man was suffering from hypothermia.
"Police would like to thank members of the public for their assistance during and after the incident, along with the Auckland International Airport Rescue Fire Service," they said.
"This reinforces the importance of being prepared when undertaking water sports. We encourage people to wear appropriate clothing, have a waterproof means of communication, and let others know your plans so if you encounter unexpected
issues the authorities can be informed."