Mountain watersheds exhibit particularly complex hydrographic networks characterized by both a high spatial and temporal environmental heterogeneity linked to the dynamic of the different water source contributions (glacier and snow meltwater, groundwater, rain). Mountain freshwater ecosystems shelter a singular biodiversity characterized by rare species, often endemic, and display a high spatial variability in aquatic community composition linked to this high level of habitats availability. However, these ecosystems are threatened by the ongoing climate change and associated flow alterations linked to both the accelerated glacier shrinkage and the modification in snow cover. In addition, although mountain regions were historically assimilated to water towers of the surrounding low lands with unlimited water resources; these regions are on the contrary facing unprecedented anthropogenic pressures on the resource, especially due to the current boom in hydropower projects but also the growing water needs of ski resorts for drinking water and artificial snow particularly during low-water periods. These flow alterations induce changes in the hydrological regime at the local scale; but also affect, at the catchment scale, the environmental heterogeneity in habitats and the connectivity of the stream network. These multi-scale alterations might have considerable effects on both the structure and functioning of mountain aquatic ecosystems. In this study, we examined the spatial distribution of aquatic invertebrate communities in two mountain glacierized catchments, with low (3%) and high (30%) glacial influence located respectively in the Andes and the Alps. We sampled benthic invertebrate communities and characterized geographical, physico-chemical and food resource conditions in 51 and 29 stream sites in the Andean and Alpine catchment, respectively. Using both distance decay relationship and variation partitioning analyses, we evaluated the relative contribution of local environmental conditions and spatial processes in structuring the aquatic metacommunity. This study allowed a better understanding of the mechanisms driving the spatial organization of the aquatic communities. This knowledge would permit to develop multi-scale environmental flows in mountains watersheds and management tools to mitigate the impacts of flow alteration and maintain these mountain freshwater ecosystems and their resulting ecosystems services.