GIS-based approach to find the suitable sites for surface flow constructed wetlands was employed for the Lithuanian river basins with low ecological status. According to the nature of the analysed criteria the flowchart consists of two phases. Criteria used include hydrographical network, soil properties, terrain features, land use, etc. Some of them have strictly defined values (constraints), and other ranges within certain limits (factors). Limited criteria were analysed using rejection principle and influencing factors using proximity analysis and overlay methods. Selecting the potential sites using standard GIS analysis tools there was estimated about 3286 sites for possible wetlands with the mean area of inflow basin about 4 km2 in the basins of water bodies at risk.