Hydropeaking, by artificially generated flow peaks, influences hydro-sedimentary dynamics on rivers and, consequently, affects bed material entrainment and transport. This study examines the onset of motion of sediment particles in four sections of a Pyrenean gravel-to-cobble bed river exposed to frequent hydropeaking (once per day, on average). Five criteria of particle entrainment have been used to assess the prediction of the initiation of grain motion at-a-section scale. Theoretical entrainment conditions were validated using real observations of mobility by means of tracers. It was found that the maximum flow discharged by the hydropower plant mostly affects the furthest downstream section, located almost 17 km downstream, in which the finer fractions of the bed are entrained. The mobile grain sizes include up to coarse gravels (≈ 30 mm). Differences in sediment supply (imposed by tributaries), the value of the bed slope and the structure of the coarse surface layer decisively control the downstream variability of incipient particle motion between sections. Results from a 17 km study segment indicated that hydropeaking generate partial transport, that is, a partially size-selective transport that occurs downstream from the hydropower plant and winnows the sand and small gravel further downstream, increasing armouring and depleting fine sediments.