We evaluated the concordance between assemblages of Ephemeroptera and Trichoptera to verify if they respond similarly to environmental gradients in the basin of Suiá-Missu river in Mato Grosso, central Brazil. We tested the predictions that: (i) the distributional pattern of mayfly and caddisfly larvae is concordant along the spatial and (ii) environmental variation along the basin, and if (iii) taxa are concordant between themselves along the seasons and with the environmental gradients disregarding the seasons of the year. We found a concordance between species composition of mayfly and caddisfly in fall-water and rainy period, when analyzed separately by each season. The concordance between environmental variables and the two taxa analyzed separately also was concordant, but only on the fall-water season. Finally, we found congruence when both analyzed groups disregarded the temporal effect, but it was less representative than when we consider the seasons variation. Our results suggest that the hydrological cycle could be a driver of changes in species composition of mayflies and caddisflies.