Mountainous running water ecosystems are vulnerable to climate change with major changes coming from warming temperatures. Species distribution will be affected and some species are anticipated to be winners (increasing their range) or losers (at risk of extinction). Climate change vulnerability is seldom integrated when assessing threat status for lists of species at risk (Red Lists), even though this might appear an important addition in the current context. The main objective of our study was to assess the potential vulnerability of Ephemeroptera (E), Plecoptera (P) and Trichoptera (T) species to global warming in a Swiss mountainous region by supplementing Species Distribution Models (SDMs) with a trait-based approach, using available historical occurrence and environmental data and to compare our outcomes with the Swiss National Red List. First, we used nine different modelling techniques and topographic, land use, climatic and hydrological variables as predictors of EPT species distribution. The shape of the response curves of the species for the environmental variables in the nine modelling techniques, together with three biological and ecological traits were used to assess the potential vulnerability of each species to climate change. The joint use of SDMs and trait approach appeared complementary and even though discrepancies were highlighted between SDMs and trait analyses, groups of potential “winners” and “losers” were raised out. Plecoptera appeared as the most vulnerable group to global warming. Divergences between current threat status of species and our results pointed out the need to integrate climate change vulnerability in Red List assessments.