This study investigated the effects of environmental variation on assemblages of dragonfly larvae (Odonata). We hypothesize that there is a significant correlation between species richness, species composition, and abundance of Odonata individuals, and habitat integrity and abiotic variables. To test this hypothesis, we sampled odonate larvae at 12 streams in the Suiá-Miçú River basin in Mato Grosso, Brazil, during three different periods of the year. Local physical and chemical variables (temperature, pH, turbidity, electrical conductivity (EC), dissolved oxygen (DO), total dissolved solids (TDS), and oxidation reduction potential (ORP)) were measured at each site using a multi-parameter probe, and integrity was assessed using the Habitat Integrity Index (HII). The variation in richness, abundance, and composition of Odonata species was related to the environmental variables analyzed, primarily by the abiotic factors pH, electrical conductivity, dissolved oxygen, total dissolved solids, and oxidation reduction potential. Our hypothesis was corroborated for the suborder Anisoptera, which showed a significant relationship with these variables, whereas Zygoptera was only related to pH. Our results show the importance of physical and chemical conditions in ecological studies using Odonata larvae as tools for the management and conservation of freshwater ecosystems.