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 examined 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 changes in flow regime under global warming. Based on long-term observational studies, we showed that the benthic fauna was highly adapted to the natural flow fluctuation and displayed both resistance and resilience to high-flow events. On the contrary, a 4-year flow manipulation study indicated that the benthic ecosystem was affected by low-flow conditions. Flow reduction induced a rapid shift in invertebrate community composition characterized by an increase in generalist species density while the system required 30 times longer to return to its initial state. Our studies suggested that the increase in frequency of low-flow events might prevent communities to fully recover leading to irreversible shifts. Thus, the reduction in glacier runoff might induce a homogenization of the aquatic fauna in glacierized catchments, leading to a reduction of the remarkable mountain stream biodiversity.