Given the importance of groundwater for food production and drinking water supply, but also for the survival of groundwater dependent terrestrial ecosystems (GWDTEs) it is essential to assess the impact of climate change on this freshwater resource. In this paper we study with high temporal and spatial resolution the impact of 28 climate change scenarios on the groundwater system of a lowland catchment in Belgium. Our results show for the scenario period 2070–2101 compared with the reference period 1960– 1991, a change in annual groundwater recharge between −20% and +7%. On average annual groundwater recharge decreases 7%. In most scenarios the recharge increases during winter but decreases during summer. The altered recharge patterns cause the groundwater level to decrease significantly from September to January. On average the groundwater level decreases about 7 cm with a standard deviation between the scenarios of 5 cm. Groundwater levels in interfluves and upstream areas are more sensitive to climate change than groundwater levels in the river valley. Groundwater discharge to GWDTEs is expected to decrease during late summer and autumn as much as 10%, though the discharge remains at reference-period level during winter and early spring. As GWDTEs are strongly influenced by temporal dynamics of the groundwater system, close monitoring of groundwater and implementation of adaptive management measures are required to prevent ecological loss.