Environmental characteristics and spatial distances between sites have been used to explain species distribution in the environment, through Neutral (space) and Niche theory (environment) predictions. We evaluated the effects of spatial and environmental factors on Odonata larvae distribution along the Suiá-Missú River Basin, state of Mato Grosso. We tested the hypotheses that (1) the environment is the main factor structuring the community due to its ecophysiological requirements; and (2) the pattern, if present, is clearer for Zygoptera. Samples were made in 12 sites on the Suiá-Missú River Basin in three seasons (2007/2008), with a total of 1.382 Odonata larvae, comprising 10 families, 51 genera and 100 morphospecies. The Anisoptera were more abundant than Zygoptera, comprising 81% of all specimens. The environment affected Zygoptera (R=0.291; p=0.007) and was the main factor structuring the assembly. Thus, Niche theory was confirmed. The absence of this effect on Anisoptera may be due to the ecophysiological adaptations that enable it to occupy different habitats. Zygoptera larvae are indicators of changes in habitat structure. The effects of environmental variables on larvae ecology emphasize the strong relationship between these organisms and environmental integrity.