Climatic seasonality provokes considerable variability in the physical conditions of streams. Although few studies have assessed systematically the temporal effects of climate on aquatic communities, the diversity and structure of odonate larval assemblages (suborders Anisoptera and Zygoptera) are predicted to be influenced by seasonality. To evaluate this hypothesis, we tested the predictions that (1) the genera and abundance richness of zygopteran and anisopteran larvae will decrease during periods of high precipitation, (2) the genera richness and abundance of the two suborders will be associated inversely with temperature, and (3) the composition of the zygopteran assemblage will be more affected by seasonality, in particular precipitation, than that of the Anisoptera, whose composition will be influenced primarily by temperature. We collected odonate larvae every three months over a 6-year period at a stream located in the Cerrado-Amazon forest transition zone and compared these data with data on the local climate from the same period. Our results indicate that the seasonal variation in precipitation had a significant effect on the abundance of both odonate suborders, but that, while the anisopteran genera richness was affected by precipitation, the zygopteran richness was not. We showed that temperature affected the abundance of both suborders, but had no effect on genera richness. As we predicted, the composition of the zygopteran larval assemblage was affected more by the climatic variables than the Anisoptera. In addition, while the Zygoptera were affected primarily by precipitation, the Anisoptera were influenced most by temperature. The results indicate that the timing of the emergence of odonate larvae is synchronized with the months preceding the rainy season, when a high density of larvae are recorded, which may reflect a strategy for both the avoidance of the effects of fluctuations in water levels and the exploitation of the relatively abundant food sources found in the terrestrial environment. Temperature also appears to contribute to this synchrony, by either accelerating or delaying the process of larval emergence.