In Switzerland, the mean annual temperature has increased by approximatively 2°C since 1864, for the most part in the last 40 years, and the temperature is expected to keep increasing. The warming of water and the changes in the flow regime are very likely to affect freshwater ecosystems. Rivers and streams of Switzerland suffer multiple anthropogenic pressures that impact their physicochemical and morphological properties. This results in a significant proportion of running waters showing a poor biological state, and climate change imposes an additional stress to biodiversity, increasing the species extinction risk. So far, no study has formally predicted (i.e. through predictive models) the potential impacts of climate change on Swiss river and stream biodiversity. Despite all the uncertainties inherent to any modelization process in ecology, this thesis aims at filling this gap using niche-based models, and at offering a countrywide insight into the running water biodiversity in the face of climate change. More generally, it informs about the main drivers of stream biodiversity of temperate mountainous regions that are impacted by human activity, and provides insights into the relative importance of the climate change threat for running water ecosystems.