Otago Harbour is the natural harbour of Dunedin, New Zealand, consisting of a long, much-indented stretch of generally navigable water separating the Otago Peninsula from the mainland. They join at its southwest end, 21 km (13 mi) from the harbour mouth. It is home to Dunedin's deep water port facilities on its western shores in the suburb of Port Chalmers.
The harbour was formed from the drowned remnants of a giant shield volcano, centred close to what is now Port Chalmers. The remains of this violent origin can be seen in the basalt of the surrounding hills. The last eruptive phase ended some ten million years ago, leaving the prominent peak of Mount Cargill.
Substantial container port facilities exist at Port Chalmers, 9 km (6 mi) along the western shore from the harbour mouth. A channel along the western side of the harbour is regularly dredged, allowing vessels with a draught of 12.5 m to Port Chalmers, and 8 m all the way to the heart of Dunedin. New Zealand's frozen meat export trade was inaugurated at Port Chalmers in 1882. The dredging of this channel, the Victoria Channel, was a major undertaking for the settlement of Dunedin in the 19th century. The eastern side of the harbour is shallow, with large sandbanks exposed at low tide.
Two islands form a line between Port Chalmers and Portobello in the lower harbour—Goat Island and Quarantine Island/Kamau Taurua. A smaller island known as Pudding Island (Titeramoa) lies close to the Peninsula shore and can be reached by foot at low tide.
Portobello is home to one of New Zealand's leading marine research establishments, the Portobello Marine Laboratory, a department of the University of Otago. This lies at the harbour's edge on the tip of a small arm of the Otago Peninsula, the Portobello Peninsula.
Near the mouth of the harbour lies the township of Aramoana (Maori for "pathway to the sea"), infamous for a massacre of 13 people by a gunman, David Gray, in November 1990.