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.