The presented methodology for regional soil water analysis was originally developed for Beerze- Reusel drainage basin in the southern part of the Netherlands. We further develop this methodology for hydrological modelling in particular combining GIS-based structural 3-D modelling with data management as a pre-processing tool for the finite element analysis of hydrosystems. The 3-D structural modelling is based on typical geological layer information. The topography of all geological layers is represented by contour maps based on which stratified finite element meshes are mapped successively. The second new development is the integration of GIS database information into the finite element analysis within the scientific OpenGeoSys (OGS) software. Thus, for example, information about complex soil systems can be incorporated into the set-up of the corresponding finite element model for the soil compartment. As an application, we present a case study for the Meijiang area with the focus on surface/subsurface water interaction and the recharge response from surface infiltration to groundwater with different time series discretization. The numerical model was implemented within the framework of object-oriented programming.