The Doubs turns after its source first northeast through Pontarlier, flows through in its course the border reservoir Lac de Moron in the direction of Delémont, where he forms the border with Switzerland from Les Brenets. It crashes over the Saut du Doubs, a 27 m high waterfall, and then flows on a short piece of about 29 km entirely on Swiss territory. This section of the river is called Clos du Doubs. After Saint-Ursanne, the river changes direction to the west and leaves the Swiss territory at Ocourt and La Motte on the Swiss side and Brémoncourt on the French side.
A special feature is the border of the Doubs along the French-Swiss border. Unlike in rivers otherwise common, the border does not run in the middle of the river, but the Doubs belongs there entirely to France. This resulted from treaties between the Prince-Bishop of Basel and the King of France.
Flowing west from Saint-Ursanne, the Doubs returns to France and flows below Saint-Hippolyte, where it takes on Dessoubre on the left, through a Montagnes du Lomont valley north to Audincourt. Here he takes right after the Allaine, then turns in its lower reaches to the southwest and strives over Baume-les-Dames, Besançon and Dole, where he takes on the left Loue, the Saône, in which he in 170 m height in Verdun-sur-le-Doubs about 16 km northeast of Chalon-sur-Saône opens.