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Assessing the impacts of groundwater abstractions on stream ecosystems is crucial for developing water planning and regulations in lowland areas that are highly dependent on groundwater, such as Denmark. To assess the effects of groundwater abstractions on flow regime and stream biota in a lowland groundwater-dominant catchment, we combined the SWAT-MODFLOW model with flow-biota empirical models including indices for three key biological taxonomic identities (fish, macroinvertebrates, and macrophytes). We assessed the effects of the current level of abstractions and also ran a scenario for assessing the effect of extreme groundwater abstractions (pumping rates of the drinking water wells were increased by 20 times in one subbasin of the catchment). Three subbasin outlets representing stream segments of different sizes were used for this evaluation. Current groundwater abstraction level had only minor impacts on the flow regime and stream biotic indices at the three subbasin outlets. The extreme abstractions, however, led to significant impacts on the small stream but had comparatively minor effects on the larger streams. The fish index responded most negatively to the groundwater abstractions, followed by the macrophyte index, decreasing, respectively, by 23.5% and 11.2% in the small stream in the extreme groundwater abstraction scenario. No apparent impact was found on macroinvertebrates in any of the three subbasin outlets. We conclude that this novel approach of a combined modelling system is a useful tool to quantitatively assess the effects of groundwater abstractions on stream biota and thereby support water planning and regulations related to groundwater abstractions. We highlight the need for developing improved biotic models that target specifically small headwater streams, which are often most affected by water abstraction., (Copyright © 2019 Elsevier B.V. All rights reserved.)