Sediment accumulation in reservoirs is frequently a problem, impelling dam managers to implement strategies such as drawdown flushing to limit siltation. Drawdown and other sediment removal methods may induce riverbed clogging downstream of dams, especially in river sections where water is diverted, thereby reducing transport capacity. In this study, we investigate the effects of drawdown flushing downstream of the Plan d'Arem run-of-the-river dam (Upper Garonne, Spain -France border) using an adaptive inter-site comparison strategy to consider a range of spatial and temporal conditions, which allow us to separate the effects of dam storage and flushing from other potential factors. Drawdown flushing has been undertaken three times during the study period over a short span of time (2 months). We couple bed material sampling, which provides direct information on bed composition, with airborne infrared thermal imaging to better interpret whether fine sediment interstitial storage within the bed is associated with clogging. We also measure bed surface grain size and bed mobility in order to investigate their potential role in controlling fine sediment dynamics. We identify surface grain size and water diversion as the main factors controlling fine sediment spatial distribution, with coarse-grained bed-surfaces and by-passing promoting fine sediment enrichment. As a result, sites located upstream and within the bypassed reached of the Plan d'Arem dam show higher fine sediment interstitial storage than sites downstream from the by-passed reach. Results from thermal imagery demonstrate such interstitial storage does not induce clogging effect. The reaches with the most important sediment storage host a high number of cool-water patches, indicating water exchanges with the hyporheic zone. Post-flushing bed composition indicates systematic export of fine sediments from the bed matrix at all sites after the first operation, afterwards fine levels remain low after the second and the third flushing. The low impact of dam flushing in term of clogging is interpreted by the fact that the interstitial material is very sandy.