The paper has two main aims. Firstly, to postulate a physical geodatabase model of a geomorphological information system based on the already existing logical geodatabase model. Secondly, to define processes of geomorphological analysis based on the physical geodatabase model. The structure of the physical model follows the logical model and is divided into three parts: adopted layers (hydrology, geology, topography and others), basic layers (elementary forms, digital elevation model and derivatives, documentation materials, genetic groups of landforms, morphodynamic phenomena, basin based features and geomorphic network) and special layers (morphostructural analysis, comprehensive geomorphological analysis and so on). The geodatabase modelling methodology was used for developing the physical geodatabase model. The geomorphological analysis is based mainly on the layer of elementary forms (defined according to their morphology and morphometry) and the derived layer of morphogenetical forms (determined by genesis of landforms). The traditional methods of geomorphological mapping and also more recent concepts of geomorphological analysis were used. The concept is presented in the context of research in the surroundings of Prášilské jezero (lake) in the Šumava (Mts.). ESRI products were used to carry out the project.