The first occurred when a boat towing a rubber tube back to the shore collided with a stationary boat by the beach at Glendhu Bay.
Queenstown Lakes District Harbourmaster Marty Black said both people hurt in the incident were riding on the tube and suffered moderately serious injuries.
They were airlifted to Lakes District Hospital by helicopter.
The second incident happened about an hour later at the boat ramp at Waterfall Creek, when a boat was being loaded onto a trailer.
Mr Black said a wave lifted the boat and pushed it forward, and a woman standing at the front of the vessel received facial and other injuries.
She was taken to the Wanaka Lakes Health Centre by ambulance.
"That was a freak accident," Mr Black said, "but both today's incidents underscore the need to always be very vigilant around boats."
Mr Black said the initial collision between the incoming boat and the parked vessel was a reminder to all boaties to keep a careful lookout at all times.
Lake Wanaka was very busy today, with an estimated 2000 small vessels on the water.
"There are a lot of boats around - I've never seen it so busy," he said.
