Formed by the east and west branches of the river, the headwaters of the Buffalo River rise in the Barry Mountains below Mount Selwyn and The Razor at an elevation exceeding 1,300 metres (4,300 ft) above sea level. The east and west branches of the river reach their confluence within the Mount Buffalo National Park, where the watercourse becomes the Buffalo River. The river flows generally north, much of its course through the remote national park, joined by nine tributaries including the Catherine River and the Dandongadale River, before reaching its confluence with the Ovens River west of the town of Myrtleford and adjacent to the Great Alpine Road. The river descends 228 metres (748 ft) over its 65-kilometre (40 mi) course.
The river is impounded by the Buffalo Dam that creates the 24,000-megalitre (5.3×10^ imp gal; 6.3×10^ US gal) reservoir, called Lake Buffalo, that was completed in 1965 and suppliespotable water to Myrtleford and irrigation of the Goulburn Valley.