In 1883, he was sent to reconnoiter the Yukon River by the US Army. Going over the Chilkoot Pass, his party built rafts and floated down the Yukon River to its mouth in the Bering Sea, naming many geographic features along the way. At more than , it was the longest raft journey that had ever been made. Schwatka's expedition alarmed the Canadian government, which sent an expedition under George Mercer Dawson to explore the Yukon in 1887. After his resignation from the army in 1885, Schwatka led two private expeditions to Alaska financed by William D. Boyce and three to northeastern Mexico and published descriptions of the social customs and the flora and fauna of these regions.