Changes in environmental characteristics can affect habitat use by birds, impacting the number of individuals, number of species, and changing species composition and functional structure of assemblages. Metrics that evaluate the functional structure of biological assemblages constitute a complementary tool to the traditional taxonomic approach, because they quantify the differences between species by means of functional traits. We assessed the effect of environmental characteristics on the taxonomic diversity (species richness, species composition and number of individuals) and functional structure (functional richness, functional evenness, Rao’s functional diversity, and community-weighted mean traits) of bird assemblages in northern Mato Grosso state, in the southwestern Brazilian Amazon. We sampled birds in 32 plots. At each plot birds were captured using mist nets, and eight environmental variables were measured: canopy openness, leaf litter, elevation, number of trees in three classes of DBH, soil clay content, and distance to nearest stream. To evaluate functional structure, we measured seven morphological traits from individuals of each bird species. Habitat variables had a significant effect on taxonomic diversity. However, the general functional structure was not affected. Elevation and distance to nearest stream were the main variables driving changes in taxonomic diversity and had a minor effect on functional richness. The other metrics of functional structure were not significantly affected by the set of environmental variables. Our results suggest that the sampled bird assemblages exhibit some functional tolerance (redundancy) to small-scale environmental variation, implying certain resilience to ecosystem modification.