A regional tectono-geomorphic analysis indicates a Pliocene to recent rock uplift of the outermost segment of the Jura fold-and-thrust belt, which spatially coincides with the intra-continental Rhine-Bresse Transfer Zone. Elevated remnants of the partly eroded Middle Pliocene Sundgau-Forêt de Chaux Gravels identified by heavy mineral analyses allow for a paleo-topographic reconstruction that yields minimum regional Latest Pliocene to recent rock uplift rates of 0.05 ± 0.02 mm/year. This uplift also affected the Pleistocene evolution of the Ognon and Doubs drainage basins and is interpreted as being tectonically controlled. While the Ognon River was deflected from the uplifted region the Doubs deeply incised into it. Focused incision of the Doubs possibly sustained ongoing deformation along anticlines which were initiated during the Neogene evolution of the thin-skinned Jura fold-and-thrust belt. At present, this erosion-related active deformation is taking place synchronously with thick-skinned tectonics, controlling the inversion of the Rhine-Bresse Transfer Zone. This suggests local decoupling between seismogenic basement faulting and erosion-related deformation of the Mesozoic cover sequences.