In order to meet the requirements established by the European Directive (2006/118/EC) on the groundwater protection, the Geological Survey of Belgium (GSB) has started a new Geographic Information System (GIS) project called Hydrobrux. The aim is to create a thorough three-dimensional geological model of the subcrop of Brussels. The latter will be used to produce a hydrogeological model of the Brussels Formation aquifer composed of sands and covering 126 km2 in the eastern part of the Brussels-Capital Region and subsequent deeper aquifers (Palaeocene and Upper Cretaceous). The GIS 3D model is built by superposition of interpolated surfaces, which represent the top surface of each modelled geological layers. Eleven top surfaces are generated independently and are based on the interpolation of 5169 points. This high density of information is provided by 2426 boreholes, water wells, outcrops, cone penetration tests (CPT) and other sources of stratigraphic data that were collected and structured in a relational database under Microsoft Access. The data were exported to ArcGIS for the geostatistics (2D mapping) and validation parts and subsequently to ArcScene for the construction and the visualisation of the 3D model.