The ecological effects of dams on sediment and river flow have been subject to an increasing attention, leading to the implementation of mitigation measures such as environmental flow release and sediment replenishment. However, fine sediment dynamics have been subject to less attention. To prevent fine sediment accumulation and maintain reservoir capacity, dam operators conduct sediment flushing operations that can release a significant amount of sediment into the downstream river, potentially damaging the ecosystem and clogging the riverbed. These flushing operations raise questions about their frequency, magnitude, and duration in order to minimize losses to the dam operator while ensuring that the downstream river maintains or improves its ecological services. From a clogging perspective, research is needed to investigate the various options available and their effects on fine sediment dynamics. In this study, the influence of a sediment flushing event on the clogging of riverbeds is analyzed using flume experiments, with a focus on the mobilization of the substrate and the conditions during the falling limb of the hydrograph. Four different scenarios have been tested using silt size sediment in suspension flowing over a bed composed of sand and gravel ranging between 0.1 and 8 mm. Scenarios are characterized by different durations of mobilization phase and falling limb, with different decrease of the suspended sediment concentration during this last phase. The experimental setup allows for the measurement of the permeability of the bed, associated with the presence of an infiltration flow, as well as the vertical distribution of silt in the bed. It appears that the mobilization of the substrate limits the effect of fine sediment on the permeability of the riverbed, although deposition is still taking place. At the end of each flushing event, the permeability was lower in the absence of mobilization. However, mobilization promotes the deposition of fine sediment below the active layer, where fine sediment forms a dense layer. The duration and concentration are key variables to limit the clogging of the substrate below the bed mobilization threshold. When the concentration and flow conditions decrease faster, a smaller reduction of the permeability is observed. Finally, a scenario characterized by low flow conditions followed by the mobilization of the substrate to declog the bed showed a limited impact of the fine sediment deposition while reducing the water volume of the flushing event. This research, although limited to some specific cases, shows that the design of sediment flushing events has an influence on the clogging of the riverbed. The deposition of silt under mobilized bed conditions reveals different results in comparison with a static bed. More research is however needed to take into account the large variety of situations that can arise in riverbeds.