The Geology collection includes collections of rocks, minerals, and meteorites and tektites. A major part of the rock collection consists of hand specimens of mid-Tertiary limestones from across northern Australia, and other specimens representing the geological history of northern Australia. The Mineral collection includes the Stockham Collection of mainly NT minerals, and the McLaughlin Collection, which is international in scope.

The meteorite and tektite collection consists mainly of NT irons (Henbury and Boxhole) and Hukitta palassite, with small meteorites and tektites and impactites making up the rest. Meteorite and tektite material is protected in the Northern Territory under the Meteorites Act 1988, which is administered by the MAGNT.

The Palaeontological collection includes more than 10,000 specimens, most of which are vertebrates from Alcoota, Bullock Creek and Casuarina (all N.T. localities). The Alcoota and Bullock Creek collections are scientifically very significant and represent periods of vertebrate evolution not known from anywhere else in Australia.

The vertebrate fossil collection contains many important type-specimens, as well as the most complete representations of many extinct types of animals, including giant marsupial megafauna and the nearly complete skeletons of the giant bird, Dromornis stirtoni, probably the largest bird ever to roam the earth. The invertebrate fossil collection is less developed, collected only on an opportunistic basis or through donation and exchange with other institutions.