Its Māori-language name (given by the Ngāti Wai iwi (tribe)) is Whangārei-te-rerenga-parāoa, meaning "the place where whales gather".

Many early settlers and Maori used the harbour as a form of transport, and this played a large role in the establishment of Whangārei, and many of the industries in the area.

These include Portland Cement Works, Marsden Point Oil Refinery and for the extraction of coal from Kamo.

Whangarei Harbour Marine Reserve is located in an inter-tidal area between Onerahi and Waikaraka, and another around Motukaroro Island, at Reotahi, Whangārei Heads.

They carry much sediment from surrounding farmland, creating the muddy nature of the harbour, and this requires dredging in some parts for navigation purposes.