Manukau Harbour is the second largest natural harbour in New Zealand. It is located to the southwest of the Auckland isthmus, and is an arm of the Tasman Sea.

The entrance to the harbour is between Ohaka Head at the southern end of the Waitakere Ranges and South Head, at the end of a long peninsula reaching up from close to the mouth of the Waikato River. At this point, ithe harbour is only 1800 metres wide, but after a nine kilometre channel it opens up into a roughly square basin 20 kilometres in width.

Because of this, tidal flow is rapid, and a bar at the harbour's entrance makes the harbour even more dangerous. New Zealand's most tragic shipwreck occurred in 1863 on this bar when the HMS Orpheus ran aground in clear weather with a loss of 193 lives. For this reason, along with the harbour's shallowness, it is not Auckland's favoured port. This title goes to the Waitemata Harbour to the northeast.

The harbour has three main arms - the Mangere inlet at the northeast lies close to Auckland's central city area, and the inner suburbs of Onehunga and Te Papapa are situated close to its northern shore. To the south of this arm lies the Otahuhu and Mangere urban areas. This arm is crossed by the Mangere Bridge . In the southeast is the Papakura Channel, which extends into the urban area of Papakura. In the southwest a further inlet known as the Waiuku River reaches south to the town of Waiuku. Auckland International Airport is located close to the harbour's eastern shore.

Fishing is excellent with many popular species able to be caught year-round. Entry to the water is difficult with few all-tide boat ramps, often local beaches are used. Cornwallis, beside the Puponga Peninsula was the first site for the future city of Auckland. However because of fraudulent land sales and rugged conditions, the settlement was abandoned in the 1840s. The surrounding bush clad hills had vast amounts of kauri removed for milling and was shipped from a Wharf on Paratutai to either the other end of the Manukau Harbour at Onehunga for use in house building in the new city of Auckland, or along the coast to other New Zealand settlements. The last mills were abandonded in the early 1920s.