The aims of this study were to verify the suitability of in situ tests using the tropical midge Kiefferulus calligaster and to evaluate the most sensitive endpoint for the assessment of aquatic pesticide contamination. In situ tests were carried out in freshwater drainage channels (farm channels) that supply vegetable crops and receive considerable pesticide spray drift, and at channels outside farms (main channels). Moreover a pesticide-free farm was used as reference site. The endpoints analysed were: survival of the larvae, body length increment, capsule width increment, cholinesterase activity and glutathione S-transferase activity. Seasonal change was investigated as rainy season and dry season. Deleterious effects were observed at some farms especially during the rainy season when farmers apply heavier doses of pesticides. However, high mortality rates observed in main channels suggest that these water bodies are also affected by other impacts besides pesticide use. This work shows the potential of the in situ assay with K. calligaster as a tool for the environmental quality assessment of tropical aquatic ecosystems.