Protection of port areas is an important task of contributing to the safety of workers, goods and vessels located in the port area. On the global market, there are many solutions to support security services, which implements the GIS technology solutions. In regard to the fact that one of the tasks carried out by geoinformatic system for port security are, estimate of the situation, spatial analyzes or monitoring of operating unit, an important element which should be particularly noted are the digital terrain model and a numerical model of the sea bottom. Properly prepared models as well as the level of detail are directly affected to the efficiency of performing operational tasks. This paper presents the design and visualization assumptions of DTM and numerical model of the sea bottom in the geoinformatic system for port security. In the particular case of this is related to the three-dimensional visualization, which was founded to present information at different levels of detail. To develop models, authors based on data from high-density measurements: interferometry echosounder and airborne laser scanning. The final development is connected model of the sea bottom and the numerical model of the terrain and different concepts of visualization. Research work are financed from fund for science in years 2010 – 2012 as a research project.