Andean streams are becoming increasingly impacted by agricultural activities. However, the potential effects of pesticides on their aquatic biodiversity remain unassessed. In order to address this knowledge gap, we conducted an experiment over 37 days in microcosms to assess the effect of two pesticides commonly used in Ecuador (Engeo and Chlorpyrifos) on the aquatic insect Nectopsyche sp. (Trichoptera: Leptoceridae) at 0, 0.10, 5 and 10 μg L−1 concentrations. The highest concentration corresponds to the maximum concentration allowed by the Equatorian legislation. We assessed insect mortality every 24 h, with leaf litter decomposition rates of organic matter determined by deploying Andean alder (Alnus acuminata) dry leaf packs in the microcosms. We found significant mortality of Nectopsyche sp. at high concentrations of Chlorpyrifos, whereas leaf litter was not significantly affected by any of the treatments. We conclude that the environmental legislation of Ecuador might not be fully protecting aquatic biodiversity from pesticide pollution. Further studies are needed, especially when considering that the maximum permitted concentration is very likely exceeded in many areas of the country. We also suggest that the maximum permissible values should be reviewed, considering each pesticide individually.