The Clifton River is a tributary of the Eaton River, which flows into the Saint-François River which in turn flows on the south shore of the Saint-François River which in turn flows onto the south shore of the St. Lawrence River. The Clifton River flows through the municipalities of Saint-Malo, Saint-Isidore-de-Clifton and Newport, in the Le Haut-Saint-François Regional County Municipality (MRC), in the administrative region of Estrie, in Quebec, in Canada.