The last decade it has been realised that climate and global change can (and very likely will affect) groundwater reserves. This will have impact on both the economical (groundwater exploitation) and ecological (ecosystems) aspects of aquifer systems. A key issue is the intrinsic variability in hydrodynamics due to natural fluctuations of meteorological conditions. In this paper the results of a modelling study are presented that reconstructs the hydrodynamic evolution of the important Neogene aquifer system in North-East Belgium, between 1833 and 2005. Boundary conditions are defined on a monthly basis. The results show that besides the yearly seasonal fluctuations also multi-year to decadal variations occur. These are especially important in the topographic higher regions like on the Campine plateau and the Campine cuesta, and can severely affect local groundwater dependent ecosystems as found in some protected areas and nature reserves. The same cyclicity is recognized in the intensity and extent of seepage of deep Neogene groundwater in the Nete basin.