Glacier-fed streams display very specific flow regime characterized by a strong temporal variability at various temporal scales due to the complexity of the water storages and releases by glaciers. However, the acceleration of glacier shrinkage under the ongoing climate change results in a strong alteration of glacier runoff. In particular, we expect an increase in both low and high extreme flow events. In a tropical glacierized catchment, we examine the relationship between flow fluctuation and aquatic community composition from the diurnal to the inter-annual time scales to identify the mechanisms driving the community structure and predict the aquatic biodiversity response to potential changes in flow regime under global warming. Based on observational and experimental studies, we show that the benthic fauna is highly adapted to the natural flow fluctuation and display both resistance and resilience to high and low flow events. However, our studies suggest that an increase in frequency of those extreme flow events might prevent communities to fully recover leading to irreversible shifts; and that reduction in glacier runoff would strongly affect the remarkable mountain stream biodiversity.