The Elizabeth River and Blackmore River catchments together occupy an area of 1,150 square kilometres (444 sq mi),[3] with the Blackmore catchment occupying 848 square kilometres (327 sq mi).

The estuary formed at the river mouth is tidal in nature and in near pristine condition.

[4] The climate of the Blackmore River region is monsoon tropical with two distinct seasons: the Dry and the Wet.

Peak flow for the Blackmore River occurs in February with 605Ml/day, after which it slowly decreases until July when there is no freshwater input into Darwin Harbour until the onset of the following wet season (Padovan 1997).

[2] The water quality at the upper estuary and freshwater monitoring sites of the Department of Land Resource Management of the Northern Territory Government was 2011 in moderate condition.