We conducted a field experiment to evaluate the effects of habitat modification by aggregations of the case-building caddisfly Goera japonica Banks (Trichoptera:Goeridae) on the size structure and composition of benthic macroinvertebrate assemblages in a Japanese stream. We compared macroinvertebrate assemblages between cobbles with (intact treatment) and without (removal treatment) case aggregations of G. japonica. The total biomass of macroinvertebrates and Margalef's index did not differ between the treatments, but total abundance and taxon richness were higher in the intact treatment than in the removal treatment. Mean body length of macroinvertebrates was significantly smaller in the intact than in the removal treatment. Abundance of individuals in small (<1.55 mm body length) and medium (1.55–3.00 mm) size classes was higher in the intact treatment than in the removal treatment, but abundance of individuals in the large (>3.00 mm) size class did not differ between treatments. For 5 of the 9 dominant macroinvertebrate species, case aggregations facilitated colonization of individuals in small and medium size classes, but not of individuals in the large size class. Assemblage composition changed with habitat modification by the case aggregations. The interstitial spaces created by case aggregations of G. japonica would be at a spatial scale suitable for smaller individuals. Our results suggest that case aggregations of G. japonica cases facilitate colonization by smaller individuals of certain species. This size-dependent and species-dependent facilitation indicates that the aggregation of case-building caddisflies can change the size structure and composition of benthic macroinvertebrate assemblages.