The Gungarlin River rises below the Munyang Range, in the southern part of the Kosciuszko National Park, on the slopes of Happy Jacks Plain, approximately 3 kilometres (1.9 mi) northwest of Adaminaby. The river flows generally south southeast, then south by west, then west by south, and finally south by west, joined by two tributaries including the Burrungubugge River, before reaching its confluence with the Snowy River. The river descends 606 metres (1,988 ft) over its 31 kilometres (19 mi) course.
The Snowy Mountains Scheme captures water from the lower Gungarlin River at the Gungarlin Weir and diverts water to the Island Bend Reservoir. The Snowy Water Inquiry Outcomes Implementation Deed identifies environmental water allocations to the released from the Gungarlin Weir as part of the Snowy Montane Rivers Increased Flows. The reaches below the weir currently contain no base flow.