Climate change may affect stream ecosystems through flow regime alterations, which can be particularly complex in streams with a significant groundwater contribution. To quantify the impacts of climate change on hydrological regime and subsequently the stream biota, we linked SWAT-MODFLOW (A model coupling the Soil and Water Assessment Tool and the Modular Finite-difference Flow Model) with flow-biota empirical models that included indices for three key biological taxonomic identities (fish, macroinvertebrates and macrophytes) and applied the model-complex to a groundwater-dominated catchment in Denmark. Effects of predicted climate change towards the end of this century relative to the reference period (1996-2005) were tested with two contrasting climate change scenarios of different greenhouse gas emissions (Representative Concentration Pathway 2.6 (RCP 2.6) and RCP 8.5) and analysed for all subbasins grouped into streams of three size classes. The total water yield in the catchment did not change significantly (-1 +/- 4 (SD) mm yr(-1)) from the baseline in the RCP2.6 scenario, while it increased by 9 = 11 mm yr(-1) in the RCP8.5 scenario. The three stream size classes underwent different alterations in flow regime and also demonstrated different biotic responses to climate change. All large and some small streams were impacted most heavily by the climate change, where fish and macrophyte indices decreased up to 14.4% and 11.2%, respectively, whereas these indices increased by up to 14.4% and 6.0%, respectively, in the medium and some small streams. The climate change effects were, as expected, larger in the RCP8.5 scenario than in the RCP2.6 scenario. Our study is the first to quantify the impacts of streamflow alterations induced by climate change on stream biota beyond specific species. (C) 2020 Elsevier B.V. All rights reserved.