The Skadar Lake Region represents one of the most important centers of geodiversity and biodiversity for Western Balkan and SE Europe. The largest part of this Region has the status of the National Park since 1983. International recognition of the importance of Skadar Lake ecosystems come in 1995, when the Lake was designated as Ramsar site. The geographical information system (GIS) that we have created has provided an excellent tool for valorization and protection of all natural values and potential of Skadar Lake Region. The GIS of Skadar Lake Region is organized for the territory of about 4500 km2 and is divided (by type and format) into various data forms: Raster data: georeferenced raster topographic maps, satellite imaginary, digital model of precipitation, digital model of temperature; Vector data: geology, hydrogeology, hydrology (Adriatic sea, lakes, rivers, underground water, springs), soil, temperature, precipitation, irrigation areas, vegetation, biomes, border of protected areas, locality of important animal species, other important localities (archeological, cultural), border of NP, state border; Digital elevation model (DEM) -resolution 20m and Database. Except of ecological conservation this information system will be helpful to a wide circle of users in the areas of natural, biotechnical, technical, economic and social sciences.