Dams are ones of the main sources of anthropogenic disturbance to the ecology and geomorphology of rivers. The aim of the present study is to understand the mechanisms underlying their influence on downstream bedload transport in three gravel-bed rivers in the Morvan massif, France. The hydrological disturbance caused by four dams is examined at a short (2.4–2.7 years) and longer (21–28 year) time scale. At the short time scale, bedload displacement was monitored (RFID) at 8 study sites around the dams. Morpho-sedimentary characterization of the bed substrate was performed at the study sites and combined with analyses of the long profile evolution and the current cross profile. The flood regime has been to a varying extent durably reduced by the dams depending on their size and purpose: the mean annual maximum flood was reduced by 9 to 40% and the number of flood events by 27 to 73.5% over the 21–28 years period. Sediment availability and loose structures were found above the dams and below medium-sized dams (<10 m) with a null or moderate influence on the flood regime (configuration I). Sediment deficit, consolidated structures, bed coarsening and vegetation encroachment were observed within 20 km downstream of large dams (>15 m) influencing strongly or moderately the flood regime (configuration II). These morpho-sedimentary features significantly affect the current bedload dynamics, creating conditions more or less favorable for the mobility of the present and incoming bedload. The cumulative mean bedload distances of RFID tracers in configuration II are significantly lower (6.8–45 m) than in configuration I (78–315 m). The current flow management of the dams has only a moderate effect on the bedload distances recorded, as shown by the mean virtual bedload velocities, which confirm the different dynamics (0.42–0.91 m/d, and 0.62–6.44 m/d, for II and I respectively). Our results demonstrate how modifications of dams on flow and bedload discharge altered the downstream morphology, but also that this inherited morphology may now be the main controlling factor of bedload transport. These findings invite further discussion about the most appropriate ways to restore rivers downstream of dams when dealing with multi-decadal inherited morphological features.