Nelly Bay is a village on Magnetic Island, and a suburb of the City of Townsville, Australia. A tourism hub on the island, it is especially significant as the site of the ferry terminal, which links it to Townsville. At the 2011 census, Nelly Bay had a population of 1055.

Robert Hayles, a local entrepreneur, started tourist ventures in the bay around 1911 and in 1917 correspondence between the Townsville Harbour Board and the Queensland Marine Department notes the existence of a jetty in the bay. During the Second World War an anti-aircraft battery was built on the foreshore of the bay. While the concrete foundations of the battery still exist, they are now overgrown, and surrounded by a housing estate.

Nelly Bay Post Office opened on 1 July 1927 (a receiving office had been open from 1923), closed in 1982 and reopened in 1994.

Nelly Bay is also home to Magnetic Island's largest infrastructure development, Magnetic Harbour, also known as Nelly Bay Harbour. The development consists of a new ferry and barge terminal, with an emergency services helipad, retail services, a marina and multi-storey residential dwellings. A frequent ferry service is operated by Sunferries, with its passenger ferry to the Townsville breakwater, and Fantasea with its vehicular barge to South Townsville.

In February 1984, Bob Katter Jr., the then new Minister for Northern Development, announced the $100 million development of a harbour and marina precinct in Nelly Bay proposed by Geoff Orpin, a former Maroochy Shire Councillor who moved to Magnetic Island in 1980. At the time, the project was to be called Magnetic Keys, and Katter insisted all environmental concerns would be addressed with construction beginning within six months. However, it was another 18 months before the developer was even able to obtain the correct permission and leases to perform feasibility and environmental impact studies in the bay.

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