It runs through parts of Jasper National Park in Alberta, Canada.

The Maligne is a major tributary of the Athabasca River.

Forming from the meltwater of Replica Peak, the river heads north, passing under Mount Mary Vaux, Lysfran Peak, Mount Unwin, and Mount Charleton before emptying into Maligne Lake.

It then flows west, entering the Athabasca River.

[4] Below Maligne Lake, it is a losing stream; its flow mostly disappears underground at Medicine Lake, only to reappear downstream in Maligne Canyon.