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The growth of agricultural and mining activities in the Amazon has impacted land-use and caused significant changes in the local environmental conditions of streams. In the face of these changes, our study aimed at assessing how environmental changes affect Odonata larval assemblages in streams in the eastern Amazon. We hypothesized that habitat conditions in streams are strong predictors of Odonata larval assemblages. We sampled 30 headwater streams (1st through 3rd order) in the eastern Amazon. We corroborated our hypothesis that regional- and local-scale environmental changes are important predictors of the Odonata larval assemblage structure. These results indicate that environmental conditions within the stream channel are important to maintain Odonata larval assemblages, as they provide important resources for larval development. For new studies, we recommend the assessment of temporal dynamics to evaluate whether these patterns are stable across time. Finally, evaluating various environmental scales of the original impact is extremely relevant for preventing the deterioration of or recuperating aquatic assemblages in Amazonian streams, considering the ongoing rapid environmental changes and deforestation in the region. Here we demonstrate that in-stream environmental conditions are important to assemblage structure and this must be considered in environmental restoration plans.