Hydropower production involves significant impacts on the dynamics and continuity of river systems. In this paper we analyse the effects of hydropeaks on river-bed particle mobility along a 2-km river channel. For this, a total of four study reaches were stablished: one considered a control reach (no impact by hydropeaking) and three impacted (upstream and downstream from the confluence of tributaries). Mobility related to three hydrological scenarios considered representative of the entire flow conditions in the control and impacted reaches was investigated. Results indicate that sediment availability and dynamics proved different in the control reach to those observed downstream in reaches daily affected by hydropeaks. In the absence of large floods capable of resetting the system from a sedimentary point-of-view, only the role of tributaries during small flow events reduces the effects of hydropeaks on river-bed particles’ availability and mobility. The effects of a hydropeaked regime are not observed for the whole spectrum of grain-sizes present in the river-bed. While the structural large elements (i.e., boulders) in the channel do not move, sand and fine gravel stored in patches of the bed are constantly entrained, transported and depleted whereas, in between, medium and large gravel are progressively winnowed. Our results point out that hydropeaked flows, which are generally not considered as disturbances in geomorphic terms, initiate frequent episodes of (selected) bed mobility and, consequently, the river-bed becomes depleted of fine sediments from patches and progressively lacks other fractions such as medium gravels, all of which are highly relevant from the ecological point of view.