Climate change has the potential to alter the flow regimes of rivers and consequently affect the taxonomic and functional diversity of freshwater organisms. We modeled future flow regimes for the 2050 and 2090 time horizons and tested how flow regimes impact the abundance of 150 macroinvertebrate species and their functional trait compositions in one lowland river catchment (Treene) and one mountainous river catchment (Kinzig) in Europe. We used all 16 global circulation models (GCMs) and regional climate models (RCMs) of the CORDEX dataset under the RCP 8.5 scenario to calculate future river flows. The high variability in relative change of flow among the 16 climate models cascaded into the ecological models and resulted in substantially different predicted abundance values for single species. This variability also cascades into any subsequent analysis of taxonomic or functional freshwater biodiversity. Our results showed that flow alteration effects are different depending on the catchment and the underlying species pool. Documenting such uncertainties provides a basis for the further assessment of potential climate-change impacts on freshwater taxa distributions. The abundance of river biota and the resulting functional trait compositions of species communities are driven by environmental factors. Flow dynamics are known to regulate the species functional trait composition by determining the structure of the physical habitat and subsequent mechanisms, such as delivery of organic matter, in river ecosystems 1-4. Climate change is projected to significantly alter natural flow regimes and dynamics 5-8 , thus affecting the composition and diversity of stream macroinvertebrates 2,9. Concerns about the detrimental effects of climate change on river biota have increased in recent years 10-12. Only recently have quantitative long-term observational flow data been used to model the quantitative flow preferences of stream macroinvertebrates 10,12 , which has been applied to predict potential changes in species abundance caused by flow alterations 13. Such modeled quantitative preferences can be used to investigate the effects of flow alterations on the functional trait composition of river biota. The response of species to climate change is frequently assessed using future projected environmental data and by modeling species distributions 14. In streams and rivers, modeled flow alterations are often used to estimate potential climate change impacts on stream macroinvertebrates (e.g., the probability of occurrences or abundances) 11,12 , but little work has been done to assess the uncertainty in the projections of either flow alterations 7 or the responses of river biota 14. Instead, potential projected changes in the flow regime and their effects on river biota have been assessed according to either a single climate change scenario 12,13 or by comparing the effects of various representative concentration pathways (RCPs) 7,15-17. However, climate change predictions differ even within each RCP because different global cir...