The headwaters are in Mount Aspiring National Park, on the eastern flanks of the Southern Alps near Haast Pass, which is the saddle between the Makarora and Haast River valleys. The Makarora River flows south into the northern end of Lake Wanaka after passing the small community of Makarora. The river attracts some recreational fishing, jetboating and kayaking. Rainbow and brown trout migrate from Lake Wanaka up the river and its tributaries to spawn, mainly in autumn and winter.