From 1911–1933 the Onerahi Branch Railway crossed the upper reaches of the harbour to provide rail access to a new wharf built at Onerahi, as the existing wharf in the town basin was unreachable for some craft. This further promoted the harbour as an important feature to the development of Whangārei. In 2006, two marine reserves were opened in Whangārei Harbour. Whangarei Harbour Marine Reserve is located in an inter-tidal area between Onerahi and Waikaraka, and another around Motukaroro Island, at Reotahi, Whangārei Heads. The Motukaroro Island reserve is popular with snorkelers due to the large amount of marine life seen there.
Geography
Whangārei Harbour stretches approximately 23 km north-west from Whangārei Heads to its farthest point inland at the town basin in Whangārei central. At its widest point it is approximately 6 km wide, between Parua Bay and Takahiwai, near One Tree Point. at Port Whangārei in 1923 The harbour is heavily tidal with a tidal range of approximately 2m, with much of the harbour being shallower than this in the wider parts. This means during low tide much of the harbour is mud flats and exposed sand bars. However, at the harbour entrance, where it is only around 800m wide, and between Onerahi and Matakohe Island, where it is only around 500m wide, it is up to 20m deep and currents can be strong. This allowed for the deep waterNorthland Port to be built at Marsden Point and for the former ports at Whangārei and Onerahi to be located so far into the harbour. The main rivers flowing into the harbour are Hātea River, Mangapai River, Limeburners Creek, Raumanga Stream and Otaika Creek. They carry lots of sediment from surrounding farmland, creating the muddy nature of the harbour, and this requires dredging in some parts for navigation purposes. As the naming of the harbour indicates, southern right whales and possibly other coastal species like humpback and Bryde's whales used to gather in the harbour historically, but today it is not often to see baleen whales in the harbour due to their small population sizes and slow recoveries caused by commercial whaling by Europeans and Maoris, and illegal mass whaling operations by Soviet Union with supports by Japan. The first documented return of the southern right whales into the harbour was in 2002. Smaller cetaceans such as dolphins and killer whales can be observed in the harbour more frequently.