Bellegarde is located at the confluence of the Valserine and the Rhone.
At this spot, the water of the two rivers runs underground, and it was possible to cross both of them easily. Since the building of the Génissiat dam at Injoux-Génissiat, the level of the Rhône was raised several meters but the pertes de la Valserine are still visible.
Bellegarde lies in a valley dominated by the plateau of Retord on the west and the massif of the Grand Crêt d'Eau and the Vuache on the east. The passage created by the Rhône is the principal access to the area around Gex and the north of Lake Geneva.