The man had headed out from Port Chalmers on Sunday on his kayak across Otago Harbour when he got into trouble along the way and capsized in the swell, Senior Sergeant Craig Dinnissen said.
Police were called to help with search efforts, he said.
The man had been missing in the harbour for three hours when police were stood down and he washed to shore at Harwood on Otago Peninsula.
He was hypothermic and taken to Dunedin Hospital, Snr Sgt Dinnissen said.
Before his kayak trip, the man said on social media he decided to make it his goal for Sunday to "travel to Ōtākou by water".
True to his word, he headed out, he said.
He said the water was calm, and he had just passed either Goat Island or Quarantine Island when the rain started and channel winds picked up.
He got hit with a 1m swell, stayed upright in the first two waves, then got hit with a third unexpected wave.
The kayak capsized.
"I started sinking and the fun began," he said.
By the time his head popped out of the water, his shorts, shirt and jacket were all gone.
He had not worn a life jacket, but said "hey, I knew what I was doing".
The man spent three hours battling away in the water, swallowing saltwater while the rain, wind and large swells kept coming in.
After three hours he got to land with one arm and one leg left working.
He said he arrived "naked" with nothing but his paddle.
"Well, completed my goal . . . and I’m feeling proud.
"Definitely took a lot longer than expected, but I made it nonetheless."
Surf Lifesaving New Zealand board member Cameron Burrows said wearing a lifejacket was a "non negotiable" in New Zealand.
He said volunteers and a large rescue team were all "freezing cold" on the water searching for the man for hours.
The man was under-dressed and under-prepared for what he was attempting.
"We need to start treating water like a hazard too, because we’ve seen so many people tragically lose their lives in waterways around New Zealand, at the beach, in rivers and lakes . . . and a lot of it is preventable.
"Ultimately, we don’t want to have such a high drowning rate, or as many water fatalities as we do."
He said people needed to be prepared, check the weather conditions, and know their own ability before they head out.
"Wear appropriate clothing, personal protective equipment, all those simple things.
"We looked out on the harbour yesterday, and we saw no one was out there — so maybe if you are the only person out there, reassess."
