Kangerlussuaq occupies an alluvial flatland on the far end of the 190 km long Kangerlussuaq Fjord, straddling both sides of the Qinnguata Kuussua river estuary. East of Kangerlussuaq there is a confluence of the two major regional rivers, the Qinnguata Kuussua and Akuliarusiarsuup Kuua. The valley of the latter forms large quicksand plains. Both rivers originate from the Russell Glacier. The edge of the glacier is easily accessible and is a major tourist attraction from the town, as is the edge of the ice sheet in the Isunngua highlands to its northeast.
Highlands such as Tarajornitsut bound Kangerlussuaq from the north and south. To the southeast behind lake Tasersuatsiaq, which provides fresh water to the town, is the vast highland of Ammalortup Nunaa, the original region artificially populated with 27 muskoxen.
The town is situated about 50 kilometres (31 mi) north of the Arctic Circle.