Both were stabilised on Rangiahua before being airlifted in separate helicopters to Starship children's hospital about 9.30pm, where they landed forty minutes later.
A St John spokeswoman said intensive care paramedics cared for the children during the rescue flights.
The boy's older sister, who wasn't as seriously injured, was discharged earlier this week.
It remained unclear exactly how the children had fallen into the water, whether a relative had been with them and how long they had been in the water for.
It's not the first time someone's fallen off the Rangiahua Island wharf - about a year ago a man was painting his boat when he fell into the water.
An Auckland Council spokesperson said it had not received a report and there wasn't going to be any investigation into it.
A Great Barrier Island resident who has relatives living on Rangiahua said a handful of families lived on the island but numbers fluctuated with the time of year.