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Anthropogenic increase of fine sediment loading is one of the main pressures for rivers worldwide. Particularly, Alpine streams are increasingly facing this issue due to sediment flushing operations from hydropower reservoirs, aimed at recovering storage for preserving electricity generation. Although Controlled Sediment Flushing Operations (CSFOs) are becoming increasingly frequent, ecological indicators to adequately assess and monitor their impact on the stream ecosystem have been poorly developed. In this work, we aimed to perform a screening of currently available biomonitoring tools to evaluate the CSFO effects on the riverine biota and adequately assess its recovery, starting from the recognition of the main ecological mechanisms triggered by the mentioned activities on benthic macroinvertebrate communities. We used two independent datasets concerning two reservoirs in the central Italian Alps to investigate the temporal effects of CSFOs repeated for four consecutive years (case-study I), and the impact of a single CSFO at a seasonal scale through a before/after-control/impact approach (case-study II). Initially, we quantified the CSFO impact on the richness and beta-diversity of macroinvertebrate communities by combining multivariate and univariate statistical techniques. Then, we compared the performance of the Siltation Index for LoTic EcoSystems (SILTES), recently developed for detecting siltation impact in Alpine streams, with that of the generic index currently adopted to assess the ecological status (sensu Water Framework Directive) of the Italian rivers, and of another sediment-specific index, but developed for a different bio-geographical area. The analysis of the two case-studies demonstrated that the nestedness (i.e. taxa loss) is the primary source of biological impairment caused by CSFOs. Moreover, we found that SILTES was more effective than the other indices because of its strong correlation with the nestedness, and since it properly discriminated impaired and pristine conditions, at both multi-annual and seasonal scale. In the first case-study, a threshold in the temporal trend of this index was detected, indicating a recovery within three months. In the second one, SILTES showed a recovery to pre-event seasonal values after nine months from the CSFO, due to larger and more persistent sediment deposition. This study demonstrates that SILTES could be adopted as a benchmark to improve the management of CSFOs from an ecological viewpoint. Our findings can be extended to the management of other sediment-related activities affecting mountainous streams worldwide, and, more generally, the adopted approach can be replicated for developing new ecological tools to manage other disturbances to river environments.