Mountain ecosystems are experiencing rapid warming resulting in ecological changes worldwide. Projecting the response of these ecosystems to climate change is thus crucial, but also uncertain due to complex interactions between topography, climate, and vegetation. Here, we performed numerical simulations in a real and a synthetic spatial domain covering a range of contrasting climatic conditions and vegetation characteristics representative of the European Alps. Simulations were run with the mechanistic ecohydrological model Tethys–Chloris to quantify the drivers of ecosystem functioning and to explore the vulnerability of Alpine ecosystems to climate change. We correlated the spatial distribution of ecohydrological responses with that of meteorological and topographic attributes and computed spatially explicit sensitivities of net primary productivity, transpiration, and snow cover to air temperature, radiation, and water availability. We also quantified how the variance in several ecohydrological processes, such as transpiration, quickly diminishes with increasing spatial aggregation, which highlights the importance of fine spatial resolution for resolving patterns in complex topographies. We conducted controlled numerical experiments in the synthetic domain to disentangle the effect of catchment orientation on ecohydrological variables, such as streamflow. Our results support previous studies reporting an altitude threshold below which Alpine ecosystems are water‐limited in the drier inner‐Alpine valleys and confirm that the wetter areas are temperature‐limited. High‐resolution simulations of mountainous areas can improve our understanding of ecosystem functioning across spatial scales. They can also locate the areas that are the most vulnerable to climate change and guide future measurement campaigns.