According to tradition, Kupe, the legendary explorer, settled in Hokianga in , after his journey of discovery from Hawaiki aboard the waka (canoe) named When he left Hokianga he declared that this would be the place of his return and left several things behind including the bailer of his canoe. Later, Kupe's grandson Nukutawhiti returned from Hawaiiki to settle in Hokianga.
In the 14th century, the great chief Puhi landed just south of the Bay of Islands. The tribe of Puhi, Ngapuhi, slowly extended westwards to reach the west coast and colonise both sides of Hokianga. Hokianga is considered to be one of the oldest settlements for the Māori, and is still a heartland for the people. Rahiri, the 17th century founder of the Ngapuhi iwi, was born at Whiria pa to the south of the harbour, where a monument stands to his memory.
In this process of expansion the Ngapuhi created and maintained over centuries a complex network of walking tracks, many of which evolved into today's roads. Wesleyan and later Anglican missionaries were guided along these ancient routes to make their own discovery of Hokianga and its accessible timber resources. Their reports soon reached merchant captains in the Bay of Islands.
Captain Herd of the Providence was the first to respond, and with disgraced missionary Thomas Kendall as guide and translator, crossed the bar and entered the harbour in 1822 (the first European ship to do so) and sailed away with the first Hokianga timber shipment.
