In 2012, the hydrogeological model (HM) of Latvia has been established, by the Environment Modelling Centre team of Riga Technical University, as an element of the Latvian shared environmental information system. The 3D –body of the geological environment to be modeled is represented by 95160125 finite difference grid which plane approximation step is 500 meters. HM is established in the framework of the commercial program Groundwater Vistas (GV) which includes the worldwide used MODFLOW system for running the model. As initial information for creating the model serves a set of digital maps (elevations of geological layer surfaces, permeability of layers, boundary conditions, etc.). Elements of hydrographical network (rivers, lakes, Baltic sea) and the digital relief map serve as boundary conditions. The map is applied on the HM top surface. The digital relief controls infiltration flow through the aeration zone and also accounts for embedding in HM lakes and areas of Baltic sea [2]. Although, rivers and lakes are included in the relief, rivers are also joined with HM layers, as universal boundary conditions of the GV system. This kind of boundary conditions includes not only river water levels but also river bed conductivity elements.