Though high mountain freshwaters are generally referred as pristine ecosystems, they have been and will be affected by multifaceted anthropogenic pressures combined with the effects of the ongoing climate change. While the acceleration of glacier shrinkage and the reduction in snow cover induce a continuous, relatively slow flow reduction at a global scale; anthropogenic activities generate abrupt but local disturbances. However, the current boom in hydropower plant constructions and the growing water needs of ski resorts for drinking water and artificial snow, particularly during low-water periods, end up multiplying these local disturbances, generating thus flow alteration at the watershed scale. However, because high mountain watersheds were historically (and are still) considered as remote unspoiled areas with unlimited water resources, eco-hydrological scientific studies are scarcer in these regions and the development of management tools have been neglected. Based on observational and experimental studies in glacierized catchments in both the Alps and the Andes, we analysed the processes that drive the distribution of aquatic-invertebrate communities. Our results show that the dynamic of the different water source contribution to mountain stream networks (glacier and snow meltwater, groundwater, rain) generate a mosaic of connected habitats that engender a strong taxonomic heterogeneity at the watershed scale, through local (environmental filtering, species interaction) and spatial (dispersal limitation) processes. These studies indicate that multiple flow alterations modify both quality and availability of aquatic habitats as well as the connectivity among them, altering the freshwater community composition, function, and dynamic. Improving our understanding of the underlying processes driving these ecosystems is crucial to provide environmental flow rules for freshwaters and develop appropriate management tools to mitigate the impacts of flow alteration and maintain these ecosystems and their resulting ecosystem services.