The headwaters of the river rise at the base of the Mitchell Ranges and are fed by spring discharge from an extensive dolomite aquifer[3] that supports areas of rainforest along the banks.

The river then flows north west before crossing the Central Arnhem Road then veering north and later forming multiple braided channels and feeding the Arafura Swamp[4] before eventually discharging into the Glyde River which in turn empties into Castlereagh Bay and the Arafura Sea.

[6] It is the ninth largest river system in the Northern Territory but has the second highest end of dry season flow-rate.

[7] A range of fauna are found in the river, there are 39 species of fish including Macleay's glassfish, barred grunter, fly-specked hardyhead, freshwater sole, golden goby, northern trout gudgeon, Gulf saratoga, barramundi, oxeye herring, rainbowfish, black-banded rainbowfish, bony bream, salmon catfish, Berney's catfish, freshwater longtom, seven-spot archerfish and the sleepy cod.

The Arafura cattle station was established in 1903 by the Eastern, African and Cold Store Company on the 50,000-square-kilometre (19,305 sq mi) lease along the Goyder and Glyde Rivers.