[3] The harbour was the scene of one of the most notorious incidents in early New Zealand history, the Boyd massacre.

On 16 July 1824 on a voyage to Sydney from Tahiti, the crew and passengers of the colonial schooner Endeavour (Capt John Dibbs) stopped in Whangaroa Harbour.

An altercation with the local Māori Ngāti Pou hapū (subtribe) of the Ngā Puhi iwi resulted in an incident where Maori warriors took control of the Endeavour and menaced the crew.

The situation was defused by the timely arrival of the Ngāti Uru chief Te Ara, of Boyd fame.

[4] In February 1827, the famous Ngā Puhi chief Hongi Hika was engaged in warfare against the tribes of Whangaroa.

[5] Acting contrary to the orders of Hongi Hika, some of his warriors plundered and burnt Wesleydale, the Wesleyan mission that had been established in June 1823 at Kaeo,[6] nine kilometres from Whangaroa.

Messrs, Hobbs and Stack, and Mr Wade and wife, were 'compelled to flee from Whangarooa (sic) for their lives'.

[8] There is no actual evidence that Hongi himself plundered the mission; he was busily pursuing the enemy and being wounded.

[11] By the latter 19th century, the Whangaroa Harbour had become an important location for the kauri gum digging trade.