Alpine regions are under increased attention worldwide do their role in storing freshwater of high quality and their high sensitivity to climate change - comparable only to the poles. Riparian ecosystems in such regions, integrating water and nutrient fluxes from aquatic and terrestrial environments, host a disproportionally rich biodiversity, despite experiencing severe climate and nutrient restrictions. With climate change rapidly encroaching in the alpine biome, it is important to fully understand how the lake and its surrounding landscape elements sustain such rich ecosystems, before their functional connectivity could be seriously severed. A total of 189 glacial origin lakes in the Central Pyrenees were surveyed to test how key elements of lake and terrestrial environments work together at different scales to shape the riparian plant composition. Secondly, we evaluated how these ecotope features drive the formation of riparian communities potentially sensitive to environmental change, and assessed their habitat distribution. At each lake plant taxonomic composition was assessed together with elemental composition of water and sediment and ecosystem-relevant geographical factors. At macroscale vegetation composition responded to pan-climatic gradients altitude and latitude, which captured, in a narrow geographic area the transition between large European climatic zones. Hydrodynamics was the main catchment-scale factor connecting riparian vegetation with large-scale water fluxes, followed by topography and geomorphology. Lake sediment Mg and Pb, and water Mn and Fe contents reflected local connections with nutrient availability, and water saturation of the substrate. Community analysis identified four keystone plant communities of large niche breadths, present in a wide range of habitats, from (i) damp environments, (ii) snow bed-silicate bedrock, (iii) wet heath, and (iv) limestone bedrock. With environmental change advancing in the alpine biome, this study provides critical information on fundamental linkages between riparian ecosystem and surrounding landscape elements, which could prove invaluable in assessing future biomic impacts.