The Wildman River flows generally northeast and then east, joined by its only major tributary, the Alligator Creek.

Approximately 150 kilometres (93 mi) east of Darwin, the river follows a highly meandering course as it reaches the western fringe of the Manassie Floodplain and heads northwest.

At this point, the river's eastern bank define a 10-kilometre (6.2 mi) stretch of the western boundary of the Kakadu National Park.

The Wildman River reaches its mouth, emptying into Finke Bay in the Van Diemen Gulf of the Timor Sea.

[3] It has a mean annual outflow of 800 gigalitres (1.046×109 cu yd),[4] The estuary formed at the river mouth is in near pristine condition.