The aim of this study was to examine the relationship between the emergence patterns of various groups of aquatic insects and different hydrological discharge periods. We hypothesize that hydrological fluctuations exert a strong influence on insect emergence, even though the orders show different responses to discharge frequency. The emergence of Diptera, Trichoptera and Ephemeroptera was measured in a tropical stream with a mesh emergence net. The sampling took place every 2 days for 14 months. Based on water flow records taken throughout the sampling period nine discharge categories were defined. A significant relationship between macroinvertebrate emergence and discharge was found, and a high percentage of emergences was fundamentally concentrated within two discharge categories namely <0.352 m3.s−1 and 0.352–0.579 m3.s−1. We used a time series consisting of 60 weekly samples to describe how emergence varied in an intra-annual period. Autoregressive integrated moving average (ARIMA) models were applied to analyze the time series of data collected for macroinvertebrate order. Time-series models for Trichoptera and Ephemeroptera showed a lagging relationship between the moving average (MA) of the emergences and environmental and biological factors, which occurred one (MAI) and two (MAII) periods earlier, respectively. For Diptera, a relationship was found between emergence and discharge for the autoregressive (AR) order. The relationship was regulated by the autecology of the organisms and occurred AR two time periods earlier (AR2). This study showed that the response of macroinvertebrates to discharge can be differentiated and can produce relevant changes in biodiversity.