Emergency services were called to Papatowai, about 20km south of Owaka, about 3.15pm today.
The incident took place during a coastal paddle stage of expedition race MAGNIficent.
Video footage shows treacherous conditions for kayakers earlier in the day.
A Hato Hone St John spokesman said two patients were taken to Dunedin Hospital by helicopter, one in a serious condition and one in a moderate condition.
Acting Senior Sergeant Nathan White said emergency services received reports of four people struggling in the water near the Tahakopa River outlet.
"The four people made their way to shore and two have since been flown by rescue helicopter to hospital for follow up medical treatment."
Fire and Emergency NZ and Police Search and Rescue also attended.
In an update posted to the race's Facebook page this evening, race co-director Andy Magness said wind had come up "quite severely" while teams were on the water.
"As our safety boat was shepherding some of them around to Tautuku Peninsula, as the winds really picked up, we had another couple that were closer to the landing on Takakopa Beach, I believe, who came out of their boats, at the bar, through the waves.
"Many of them were able to make it to shore on their own.
"A couple of them were out in the water . . . they were freaked out and they hit their [Emergency Position-Indicating Radio Beacon], which is the absolute right thing to do.
"Everybody ended up making it to shore on their own, which was great."
The rest of the afternoon's paddling section was called off, due to high winds and drained resources following the rescue, Mr Magness said.
Teams had been given the option to carry on on-foot, he said.
"It was a wild hour or so, but we've been in good contact with the police and Heli Otago and they were pretty happy with the way the situation was managed, given the fact that everything went pear-shaped at once."
