Construction of multilayer numerical models in a karst-fractured medium creates big difficulties in the correct and credible presentation of groundwater flow systems. Presentation of geometric groundwater medium using data from 2D geological maps, bore holes and geological cross-sections can be insufficient without acute interpretation of deep geological structure. Applications of new techniques of computer 3D geological modelling helps better mapping and understand deep geological structure. In the paper 3D geological model of MGWB Gliwice is presented. Geological model has been developed using Earth Vision software. Possibility of presenting 3D hydrogeological formation in geological structure model with many horsts and grabens separated by faults will be have significantly influenced on correctness digitizing hydrogeological medium structure in the flow model FeFlow.