He also quoted the Whanganui saying "I am the river and the river is me" and said it was "an extraordinary privilege" to be asked to travel on a waka on the river today.
A crowd of about 300 people including media gathered on the marae.
Before embarking on the waka journey, Prince Harry greeted the waka crew and posed for a photo while crowds of people on either side of the river waited.
The waka left from the Putiki slipway, with the Prince seated near the back.