It continues through an estuarine area and discharges into the East Arm of Darwin Harbour then Beagle Gulf and eventually into the Timor Sea.

[4] The climate of the Elizabeth River region is monsoon tropical with two distinct seasons: dry and wet.

The dry season lasts for six months between April and September with an average rainfall of 24 mm, whereas the wet season lasts between October and March with an average monthly rainfall of 254 mm/month (according to the Bureau of Meteorology, 1999).

Peak flow for the Elizabeth River occurs in February with 389Ml/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 Finniss, Elizabeth and Howard Rivers have a mean annual outflow of 3,000 gigalitres (3.924×109 cu yd),[5] The water quality at the upper estuary monitoring sites of the Northern Territory Government was 2011 in excellent condition.