ABSTRACT In aquatic ecosystems, benthic macroinvertebrates are strongly influenced by riparian habitat quality. We investigated associations between riparian deforestation, stream habitat variables and benthic macroinvertebrate assemblage structure, particularly sensitive taxa. We sampled macroinvertebrates and physical-chemical variables during both the dry and wet seasons at three sites, each with low, medium, and high levels of riparian deforestation, in each of three first-order streams in the lower zone of the Caeté river in eastern Amazonia, Brazil. The relationships were examined using Generalized Linear Mixed-Models (GLMM) and multivariate analysis. Macroinvertebrate families most associated with deforestation levels were determined by Indicator Species Analysis. We hypothesized that lower riparian deforestation is associated with greater diversity, especially of sensitive taxa, and lower dominance. A total of 3,427 macroinvertebrates distributed in 54 families were found, of which 25 were sensitive taxa. Sites with high deforestation, associated with Glossiphonidae, Tubificidae, and Naididae, differed from those with medium (associated with Limnephilidae) and low (associated with Polycentropodidae and Hydropsychidae) deforestation. Families and abundance of EPTC (Ephemeroptera, Plecoptera, Trichoptera, and Coleoptera) were lower at high deforestation, with significant losses of taxa compared to the whole assemblage. In Caeté headwaters, deforestation is an important factor for structuring benthic macroinvertebrate assemblages.