Global climate change (GCC) is expected to lead to massive loss of global biodiversity in the alpine regions of mountain ranges. Studies on the potential effects of GCC on low mountain areas remain sparse, however, despite the high conservation value of these areas as biodiversity refugia. We chose a species distribution modeling approach to assess potential GCC impacts on the future distributions of montane freshwater invertebrates under two different greenhouse gas scenarios and three averaged general circulation models. For this, ensemble models consisting of six algorithms [generalized linear model (GLM), generalized boosted model (GBM), generalized additive model (GAM), classification tree analysis (CTA), artificial neural networks (ANN), and multivariate adaptive regression splines (MARS)] were applied to project areas of 23 cold-stenothermic aquatic insects from montane regions of Central Europe. We found an average loss of 70–80% of the potential distribution for the study species until 2080, depending on the underlying Intergovernmental Panel on Climate Change scenario. Species distribution ranges below 1000 m above sea level were found to decrease by up to ~96% according to the severest greenhouse gas emission scenario. While the Alps remain the single main refugium under the A2a greenhouse gas emission scenario, the more moderate climate scenario B2a shows fragmented potential persistence of montane insects in some low mountain ranges. The results show that montane freshwater assemblages in low mountain ranges are particularly threatened by ongoing GCC. As vertical dispersal is limited by elevational restriction, low mountain ranges may act as summit traps under GCC. We thus propose that GCC will lead to the extinction of several species and unique genetic lineages of postglacial relict species, resulting in a significant decline in Central European fauna.