Streambed colmation by fine sediment, e.g. the deposition, accumulation and storage of fines in the substrate, is a major environmental concern throughout the world. Nevertheless, the ecological effects of streambed colmation on both benthic and hyporheic invertebrate assemblages have rarely been considered simultaneously. We studied a continuum of a naturally increasing percentage of fine sediment in three temperate rivers and hypothesized that the increasing percentage of fine sediment would decrease both benthic and hyporheic invertebrate densities and diversities, and reduce the similarities between them. To test these hypotheses, we first compared heavily, moderately and lightly clogged reaches located in downwelling areas and sampled invertebrates in the benthic zone and at 3 different depths (10, 30 and 50 cm) in the hyporheic zone. Secondly, we modified the sediment grain size distribution experimentally by increasing the percentage of fine sediment and using artificial substrates. The increasing colmation halved the hyporheic taxonomic richness and reduced benthic and hyporheic densities to a third. Some taxa were found in both zones, mainly in high colmation (e.g. Baetidae) or low colmation contexts (e.g. Orthocladiinae, Cyclopoida and Harpacticoida). The dissimilarity between benthic and hyporheic fauna (only at -50 cm) was significantly higher in heavily clogged reaches than in moderately and lightly clogged ones, suggesting reduced vertical exchange of invertebrates or differential impacts between zones. The total abundance, taxonomic richness, percentage of EPT taxa and densities of most organisms observed using the artificial substrates decreased linearly with the increasing percentage of fine sediment in the experiment. Only the Ephemeroptera Caenis spp. and Heptageniidae disappeared above 30 and 50 % of fine sediment, respectively, suggesting that the response to increasing colmation are strongly taxon-specific. High amount of fine sediments within the substrate significantly decreased habitat quality for benthic and hyporheic invertebrates and thus limit the production of streams and their capacity to recover after disturbance. Moreover, the use of hyporheic invertebrates seems more relevant than benthic invertebrates to assess the effect of colmation and thus could be tested in future research as indicators.