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It was the second small boat to capsize at the river mouth on successive weekends.
The motorboat Delilah capsized near the Motorata Island Scenic Reserve, at the north side of the river mouth about 12.30pm, and the two occupants were able to right the boat and make their way ashore.
Six local first responders, assisted by members of the public, helped the men by removing their wet clothes, warming them with blankets and hats and sitting them in cars until the rescue helicopter arrived.
Bob Lyall, co-ordinator of the 18-strong Taieri Mouth First Response Group, said a recently cut 120m-long track had provided quicker rescue access to the beach area near the mouth.
The men were brought up from the beach via the track and uplifted by the rescue helicopter, he said.
The wooden boat was in excellent condition and the men were wearing life jackets, Acting Senior Sergeant Chris McLellan said.
Otago marine search and rescue adviser Keith Simon, of Taieri Mouth, warned that conditions at bars could change quickly and reminded boat users about the risks of crossing them in small craft.
The Taieri first response group is affiliated to Dunedin marine search and rescue.