Six major watersheds drain the territory, each with several tributaries. The major watersheds are the Alsek, Yukon, Porcupine (which drains to the Yukon River in Alaska), Peel (which drains to the Mackenzie Delta), Liard (which drains to the Mackenzie Basin through British Columbia, Alberta and the Northwest Territories), and North Slope.

Yukon River Basin (including the Porcupine River Basin)

The Yukon River Basin encompasses the majority of communities in Yukon. The Yukon Headwaters contains the Southern Lakes region of Yukon and Northern British Columbia; there are glaciers throughout the mountains of these headwaters. The Teslin River joins the Yukon River north of Lake Lebarge, contributing water mainly from snowmelt runoff in the upper portions of the basin. The Pelly and Stewart Rivers drain the eastern portion of the drainage, including mountainous terrain. The White River basin includes Kluane Lake and glaciated headwaters in Kluane National Park and Preserve. The Yukon River mainstem flows past Dawson City toward Eagle, Alaska. The Porcupine River drains the Old Crow Flats and is underlain by continuous permafrost; it joins the Yukon River in Alaska.

Liard and Peel River Basins

The Liard and Peel River Basins are part of the Mackenzie River Basin. The Liard drains the Pelly Mountains of southern Yukon and flows through northeastern British Columbia to join the Mackenzie River in the Northwest Territories. The Peel River is largely controlled by mountainous and permafrost rich terrain; it flows into the Northwest Territories to its confluence with the Mackenzie River near Fort McPherson.

Alsek River Basin

The Alsek River drains the southwestern portion of the Yukon to the Pacific Ocean. It is classified as a Canadian Heritage River because of its significant natural resources: massive ice fields, high mountain peaks, unique geologic history, coastal and interior plant communities, significant grizzly bear population, and diverse bird species.

North Slope

Yukon's North Slope is characterized by the influence of the underlying continuous permafrost. Rivers in this region drain the British, Barn and Richardson Mountains to the Beaufort Sea.

 These watersheds make up the six water management areas identified in the Waters Regulation and used by the Yukon Water Board when issuing water licences.