Mountainous catchments cover a broad range of elevations and their response to a warming climate is expected to vary significantly in space. Nevertheless, studies on climate change impacts typically examine the changes in flow statistics only at the catchment outlet. In this study, we instead demonstrate the high variability of the hydrological response to climate change at the sub-catchment scale, investigating in detail the contribution of all components of the hydrological cycle in two mountainous catchments (Thur and Kleine Emme) in the Swiss Alps. The analysis was conducted with a two-dimensional weather generator model that simulated gridded climate variables at an hourly and 2-km resolution until the end of the 21st century for the RCP8.5 emission scenario. The climate ensemble was used as input into a distributed hydrological model to estimate the changes in hydrological processes at 100-m and hourly resolutions. Climate models show that precipitation intensifies during winter but weakens during summer in the order of ± 5–10% toward the end of the century. Temperature will rise by up to 4°C, leading to a 50% reduction in snowmelt, 10% increase in evapotranspiration, and shift in precipitation type from snowfall to rainfall. As a result, streamflow is projected to increase by 40% in winter but decrease by 20% to 40% during summer, with winter floods becoming more frequent. The changes to streamflow (mean and extreme low and high flows) at the sub-catchments show a strong dependency with elevation. In contrast to the small changes projected at the outlet of the catchments, streamflow shows a reduction at higher elevations (up to −20% change in mean streamflow for sub-catchments at elevations exceeding 1400 m) and an increase at lower elevations (up to +5% for Kleine Emme and +20% for the Thur at elevations below 600 m). These impacts are tied to the changes in precipitation, as well as changes in snowmelt (at high elevation) and evapotranspiration (at low elevation). The results reveal the causes and diversity of hydrological response to climate change, emphasizing the importance of investigating the distributed impacts of climate change in mountainous environments.