1. Understanding how differences in intensity and frequency of hydrological disturbances affect the resistance and resilience of aquatic organisms is key to manage aquatic systems in a fast-changing world. Organisms’ responses to environmental changes can be influenced by different life strategies. Some aquatic organisms have strategies that improve the permanence in aquatic systems, while others use strategies that enhance colonization. 2. Therefore, we carried out a manipulative experiment to understand the resistance/resilience of aquatic insects based on their functional characteristics to hydrological disturbances in streams in the Cerrado hotspot. 3. We placed 200 artificial substrates in five streams and submitted them to changing water flow regimes that differed both in frequency and intensity. Then we observed the response of the aquatic community for 39 days. We used a Hierarchical Bayesian strategy approach to estimate the probabilities of permanence and colonization of each life strategy group (nine groups). 4. We observe that the most intense changes in the water flow tend to affect the permanence of almost all groups. However, this effect was reduced in intensity over time. On the other hand, less frequent disturbances, regardless of intensity, tend to reduce the permanence of most groups of aquatic insects over time. The difference in the effect of disturbance regarding intensity (higher or lower) may be related to a greater dispersal capacity of some groups. 5. These results are worrisome in a scenario of reduced riparian vegetation around streams and with the expectation of precipitation to become more concentrated in shorter periods of time due to climate change in the Cerrado hotspot. Together, these anthropogenic changes tend to increase the effect of runoff on the lotic systems and, consequently, reduces the permanence of many groups of aquatic insects in their habitat, particularly those with traits associated with permanence.