The bay extends some 160 km from Caloundra in the north almost to Surfers Paradise in the south. The bay's southern navigation entrance is the Gold Coast Seaway.

It is separated from the Pacific Ocean by a chain of three sand islands - Moreton Island in the north, North Stradbroke Island, and South Stradbroke Island in the south. Tipplers Passage is the main channel on the western coast of South Stradbroke Island. The Gold Coast Seaway is at the southern extent of Moreton Bay, before the Gold Coast Broadwater.

The bay itself contains around 360 islands in total. This includes the populated Russell, Macleay, Lamb and Karragarra Islands collectively known as the Southern Moreton Bay Islands. Residential development has also occurred on Coochiemudlo Island and Bribie Island.

Moreton Bay is generally shallow and sandy, though a substantive channel is maintained to allow access to the Port of Brisbane at Fisherman Islands at the mouth of the Brisbane River, for international shipping. As well as the Brisbane River, the Nerang River, Pimpama River, Logan River, Pine River, Tingalpa Creek and the Schulz Canal all empty into Moreton Bay. Within Moreton Bay are the smaller bays of Waterloo Bay, Redland Bay, Raby Bay, Deception Bay and Bramble Bay.