The Mowamba River rises within The Snowy Mountains Range, part of the Great Dividing Range, contained within the Kosciuszko National Park, on the northeastern slopes of Mount Terrible.

The river flows generally south then northeast by east, joined by two minor tributaries, before reaching its confluence with the Snowy River approximately 2 kilometres (1.2 mi) south of Jindabyne, in the Jindabyne Gorge.

[1] The river descends 507 metres (1,663 ft) over its 32 kilometres (20 mi) course.

[2] Water from the Mowamba River is diverted to Jindabyne Dam via the Mowamba weir and aqueduct; that is part of the Snowy Mountains Scheme.

Since January 2006, environmental water releases to the Snowy River have occurred from Jindabyne Dam as the infrastructure upgrades to the dam wall had been completed.