Elimination of sediments from river reservoirs is a common management problem for hydroelectric power plants. Periodical flushing can have negative impacts downstream. This study investigated the impact of a flushing event on the physico-chemical changes in the downstream sections and on the consequences for the benthic macroinvertebrate community. A special emphasis was placed on trace metal fate, partitioning and speciation. The assessment of taxonomic diversity and the frequency of taxa with specific traits was used to estimate the impact on the macroinvertebrate community. Trace metals were measured in the dissolved and particulate fraction, in the surface sediment and in selected macroinvertebrates. Bioanalogical diffusive gradient thin films (DGT) complemented the approach. The results showed an increase of Al, Co, Mn and Ni in the dissolved fraction (Mdis). Crdis, Fedis, Pbdis, and Cudis showed strong spatial variation. In the exchangeable fraction of particulate metals, trends were contrasted, depending on the metal. The calculated free ion and DGT concentrations increased during the flush for all metals, except for Cu. Accumulation in invertebrates increased only in a small number of cases. Macroinvertebrate diversity was negatively impacted as shown by lower taxonomic richness and rarefied richness after the event. Trait profiles were also affected. Overall, the study revealed that flushing operations have an impact on trace metal partitioning between dissolved, suspended particulate matter and sediments, metal speciation, as well as the functional invertebrate diversity.