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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 better R2 and NSE (Nash–Sutcliffe efficiency) for SWAT–MODFLOW but slightly better PBIAS (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.

Abstract. Being able to account for temporal patterns of streamflow, the distribution of groundwater resources, as well as the interactions between surface water and groundwater is imperative for informed water resources management. We hypothesize that, when assessing the impacts of water abstractions on streamflow patterns, the benefits of applying a coupled catchment model relative to a lumped semi-distributed catchment model outweigh the costs of additional data requirement and computational resources. We applied the widely used semi-distributed SWAT model and the recently developed SWAT-MODFLOW model, which allows full distribution of the groundwater domain, to a Danish, lowland, groundwater-dominated catchment, the Uggerby River Catchment. We compared the performance of the two models based on the observed streamflow and assessed the simulated streamflow signals of each model when running four groundwater abstraction scenarios with real wells and abstraction rates. The SWAT-MODFLOW model complex was further developed to enable the application of the Drain Package of MODFLOW and to allow auto-irrigation on agricultural fields and pastures. Both models were calibrated and validated, and an approach based on PEST was developed and utilized to enable simultaneous calibration of SWAT and MODFLOW parameters. Both models demonstrated generally good performance for the temporal pattern of streamflow, albeit SWAT-MODFLOW performed somewhat better. In addition, SWAT-MODFLOW generates spatially explicit groundwater-related outputs, such as spatial-temporal patterns of water table elevation. In the abstraction scenarios analysis, both models indicated that abstraction for drinking water caused some degree of streamflow depletion, while abstraction for auto-irrigation led to a slight total flow increase (but a decrease of soil or aquifer water storages, which may influence the hydrology outside the catchment). In general, the simulated signals of SWAT-MODFLOW appeared more plausible than those of SWAT, and the SWAT-MODFLOW decrease in streamflow was much closer to the actual volume abstracted. The impact of drinking water abstraction on streamflow depletion simulated by SWAT was unrealistically low, and the streamflow increase caused by irrigation abstraction was exaggerated compared with SWAT-MODFLOW. We conclude that the further developed SWAT-MODFLOW model calibrated by PEST had a better hydrological simulation performance, wider possibilities for groundwater analysis, and much more realistic signals relative to the semi-distributed SWAT model when assessing the impacts of groundwater abstractions for either irrigation or drinking water on streamflow; hence, it has the potential to be a useful tool in the management of water resources in groundwater-affected catchments. However, this comes at the expense of higher computational demand and more time consumption.

Hydrological effects of groundwater abstraction near a Danish river valley have been assessed by integrated hydrological modelling. The study site contains groundwater‐dependent terrestrial ecosystems in terms of fen and spring habitats that are highly dependent on regional and local scale hydrology. Fens are rare and threatened worldwide due to pressures from agriculture, to lack of appropriate management and to altered catchment hydrology. A solid foundation for hydrological modelling was established based on intensive monitoring at the site, combined with full‐scale pumping tests in the area. A regional groundwater model was used to describe the dynamics in groundwater recharge and the large‐scale discharge to streams. A local grid refinement approach was then applied in a detailed assessment of damage in order to balance the computational effort and the need for a high spatial resolution. A considerable flow reduction in the natural spring was monitored during a full‐scale pumping test while no significant effects on the water table in the fen habitats were observed. A modelled abstraction scenario predicted a lowering of 2–3 cm in the centre of the main fen area during summer periods. The predicted change in water table conditions in the fen habitat is compared to the variability found in 35 Danish fens, and the ecological response is discussed based on statistical water‐level vegetation relations. The results provide a rare quantitative foundation for decision making in relation to management of groundwater‐dependent terrestrial ecosystems. Copyright © 2013 John Wiley & Sons, Ltd.