As climate change is projected to alter both temperature and precipitation, snow-controlled mid-latitude catchments are expected to experience substantial shifts in their seasonal regime, which will have direct implications for water management. In order to provide authoritative projections of climate change impacts, the uncertainty inherent to all components of the modelling chain needs to be accounted for. This study assesses the uncertainty in potential impacts of climate change on the hydro-climate of a headwater sub-catchment of New Zealand's largest catchment (the Clutha River) using a fully distributed hydrological model (WaSiM) and unique ensemble encompassing different uncertainty sources: general circulation model (GCM), emission scenario, bias correction and snow model. The inclusion of snow models is particularly important, given that (1) they are a rarely considered aspect of uncertainty in hydrological modelling studies, and (2) snow has a considerable influence on seasonal patterns of river flow in alpine catchments such as the Clutha. Projected changes in river flow for the 2050s and 2090s encompass substantial increases in streamflow from May to October, and a decline between December and March. The dominant drivers are changes in the seasonal distribution of precipitation (for the 2090s +29 to +84% in winter) and substantial decreases in the seasonal snow storage due to temperature increase. A quantitative comparison of uncertainty identified GCM structure as the dominant contributor in the seasonal streamflow signal (44–57%) followed by emission scenario (16–49%), bias correction (4–22%) and snow model (3–10%). While these findings suggest that the role of the snow model is comparatively small, its contribution to the overall uncertainty was still found to be noticeable for winter and summer.