Abstract Abiotic and biotic factors play an essential role in the structuring of natural communities. Aquatic ecosystems have complex interaction networks, encompassing predator/prey relationships and structural support. Among aquatic organisms, the order Odonata is a model group for understanding those relationships since they can be both predators and prey. Our hypotheses were that Zygoptera are (i) influenced positively by Ephemeroptera, Plecoptera and Trichoptera (EPT) and the Habitat Integrity Index (HII), and negatively by fish and macrophytes; and (ii) Anisoptera are affected positively by EPT and macrophytes, and negatively by fish and HII. We found that Zygoptera were affected by the fish functional trophic groups, while Anisoptera were affected by macrophytes, EPT, fish and HII. Macrophytes affected anisopterans positively because they provide perching sites for adults. The results for EPT and HII may be related since these organisms are also sensitive to environmental changes. More open areas have lower HII values and the negative relationship with Anisoptera may be explained by physiological constraints. The negative relationship between EPT and Anisoptera could be explained by the low occurrence of EPT in open sites, which are the sites that were highly rich in Anisoptera. Finally, the dominance of specific functional trophic groups of fish influences Odonata suborders in different ways. In conclusion, the results show the importance of ecological interactions for Odonata in Amazonian streams in both direct and indirect ways.