Māori settlements and marae have been scattered around the harbour margins for hundreds of years. The waterways of the Kaipara provided, and still provide, Māori with resources and a ready means of moving between marae.
Today most marae are associated with the Ngāti Whātua sub-tribes, Te Taoū and Te Uri-o-Hau. These sub-tribes both descend from the chief Haumoewhārangi who settled on the north end of the Kaipara entrance at Poutō. He was killed in an argument about kūmara (sweet potatoes). His widow Waihekeao developed a partnership with a Tainui warrior chief, Kāwharu. Kāwharu led several destructive campaigns around Kaipara.
Eventually the descendants of Waihekeao and Haumoewhārangi came to control the Kaipara Harbour. Te Uri-o-Hau was founded by Hakiputatōmuri, and controlled the northern part of Kaipara Harbour. Te Taoū was founded by Mawake, and controlled the south.