The Quaternary geomorphic history of southern Germany is tightly linked to the reorganisation of the drainage basins of the Danube and Rhine. Driven by the tectonic development of the Jura Fold-and-Thrust belt, by the subsidence of the Upper Rhine Graben, and by repeated foreland glaciations both rivers and their tributaries changed their courses with corresponding shifts of their drainage divides. The formation of the prominent Wutach Gorge in the Black Forest in response to a river deflection ~18,000 years ago is the youngest among a series of events and documents the highly dynamic nature and landscape-changing consequences of drainage basin reorganisation. Ongoing, more subtle divide shifts are also evidenced by cross-divide routing of subsurface flows between the Danube stream sink and the Aachtopf, Germany’s most productive spring. Geomorphometric analysis indicates that the Rhine basin will continue to grow at the expense of the Danube catchment in the future.