Geographic information systems (GIS) use is presented in the problem of sitting areas for construction of natural systems such as stabilization ponds (SPs) for domestic wastewater treatment. For this purpose, several variables, such as topography, land use, type of geological formation, distance to major rivers or lakes, distance to existing cities and villages, existence of environmentally protected areas, mean minimum monthly temperatures and required wastewater effluent characteristics were analyzed with the GIS, in order to accept or reject a particular area within a region. The method is applied in the region of Thrace (Northeast Greece) at the municipal level. The required area for SP systems was calculated in each of the 36 municipalities of Thrace (including two islands, Thassos and Samothraki) as a function of the population of each municipality, temperature and local wastewater effluent discharge criteria. Based on the GIS analysis, suitable locations were identified in each municipality first, and then the total required surface area of these systems was compared to the available surface area of each municipality, in order to decide whether SP systems could be a viable solution to the wastewater management problem in the particular region. In that way the present methodology offers a fast and simple method to check the suitability of new areas for construction of such systems.