The applications of geographical information systems (GIS) display still a number of theoretical-methodical, as well as practical problems. The article deals with the problems of unified cartographical basement and its harmonisation with different thematic information layers, with the problems of correct definition of the georeferencing elements, with the geosystem based collection, elaboration and deposition of the information to the GIS. As the methodical example of the geosystem based elaboration the GIS of the watershed of the river Ipeľ is presented, especially the way of the composition of the catalogue of the GIS and the thematic layers of information.