Lotic ecosystems are altered at various spatial scales leading to the simplification of water bodies and the dominance or exclusion of certain organisms. In streams, species may have limitations generated by the environment that result in a more abundant or rare occurrence. Thus, the aim of this study was to evaluate the influence of water physical-chemical variables and land use in the drainage basin on the composition of Ephemeroptera, Plecoptera and Trichoptera (EPT) assemblages in the streams of Atlantic Forest. We collected water samples and aquatic insects from 18 streams in Atlantic Forest in southern Brazil. We evaluated the relationship between physical-chemical variables of water and land use and the dissimilarity of EPT assemblages in three different situations: (i) matrix with all organisms collected, (ii) matrix containing only common genera and (iii) matrix containing only the rare genera. We collected 6 023 EPT larvae from 41 genera; 62 % of the individuals belonged to the order Trichoptera, 32 % to the order Ephemeroptera and 6 % to the order Plecoptera. The most common organisms (10 genera) accounted for 86 % of the total abundance of identified individuals. On the other hand, rare genera corresponded to 76 % of the total richness, but only 6 % of the total abundance. For the three matrices studied, the pH, electrical conductivity and riparian vegetation were correlated with the dissimilarity matrix of the three biological datasets used. In our study, we observed that the pH, electric conductivity, exposed soil and riparian vegetation variables were the most important for the dissimilarity of the EPT assemblages. In addition, our results demonstrated that variables at different scales (stream and riparian zone) structure stream insect assemblages.