Emergency services were alerted after the skiff capsized between Northcote and Westhaven marinas at about 8.45am.
Sergeant John Saunders of the Maritime Unit said details were scarce as staff were still at the scene.
However he said it was reported that the skiff capsized after it hit a wave created by a nearby ferry.
"We're not 100 per cent sure what happened. It's blowing fairly hard and raining thought so we're not sure if that was the cause or whether it was just a little bit rough," he said.
"Those skiffs are pretty low to the water, they're not really designed for rough water."
One person was suffering hypothermia, but Mr Saunders understood the pair were not seriously injured. They were taken to the Bayswater marina, where an ambulance was waiting.