The Saône rises west of the Vosges in the Vosges department at 405 m in the town of Vioménil. The spring emerges in a channel and feeds two water basins in a wash house below. Directly after its source, the Upper Saône runs west to Bonvillet through a forest area. From there it initially flows southwest and forms a large, narrow river loop in Monthureux-sur-Saône. At Châtillon-sur-Saône it changes its flow direction to the southeast and reaches the border with the Haute-Saône department at Jonvelle. South of Corre, after about 70 km of flow, the Saône meets the tributary Côney and the Canal des Vosges. From its confluence, the Saône is navigable and is called the Little Saône.
In the further course, cut-through canals separated from the natural course of the Saône were created in numerous places in order to shorten larger loops of the river for shipping (see shipping section). There are locks in most of these canals. At Conflandey it joins the Lanterne, and at Heuilley-sur-Saône after about 215 km the Ognon, which is approximately the same length, joins it. There the Saône crosses the border with the Côte-d'Or department. After reaching the Saône-et-Loire department, the Saône flows into its largest tributary, the Doubs, after a good 300 km. It is about 150 km longer than the Saône at this point and has more water (Doubs: 173 m³/s, Saône: 160 m³/s). From there it is called the Great Saône.
From the mouth of the Seille, the Saône forms the border with the Ain department and reaches the Rhône department north of Belleville. In Lyon it flows into the Rhône as a right tributary.