Background Groundwater abstraction can cause a decline in the water table, and thereby affects surface streamflow connected to the aquifer, which may impair the sustainability of both the water resource itself and the ecosystem that it supports. To quantify the streamflow response to groundwater abstractions for either irrigation or drinking water at catchment scale and compared the performance of the widely used semi-distributed hydrological model SWAT and an recently integrated surface-subsurface model SWAT-MODFLOW, we applied both SWAT and SWAT-MODFLOW to a groundwater-dominated catchment in Denmark and tested a range of groundwater abstraction scenarios. Results To accommodate the study area characteristics, the SWAT-MODFLOW model complex was further developed to enable the Drain package and an auto-irrigation routine to be used. A PEST (parameter estimation by sequential testing)-based approach which enables simultaneous calibration of SWAT and MODFLOW parameters was developed to calibrate SWAT-MODFLOW. Both models demonstrated generally good statistical performance for the temporal pattern of streamflow, with betterR(2)andNSE(Nash-Sutcliffe efficiency) for SWAT-MODFLOW but slightly betterP(BIAS)(percent bias) for SWAT. Both models indicated that drinking water abstractions caused some degree of streamflow depletion, while abstractions for returned irrigation led to a slight total flow increase, but may influence the hydrology outside the catchment. However, the streamflow decrease caused by drinking water abstractions simulated by SWAT was unrealistically low, and the streamflow increase caused by irrigation abstractions was exaggerated compared with SWAT-MODFLOW. Conclusion We conclude that the SWAT-MODFLOW model produces much more realistic signals relative to the SWAT model when quantifying the streamflow response to groundwater abstractions for irrigation or drinking water; hence, it has great potential to be a useful tool in the management of water resources in groundwater-dominated catchments. With further development of SWAT-MODFLOW and the PEST-based approach developed for its calibration, this study would broaden the SWAT-MODFLOW application and benefit catchment managers.