Protected areas (PA) and special protected areas (SPA) are the regions where species, especially endemic ones, are protected for their geographical locations, biotic and abiotic factors as well as biological diversity is maintained. The land use and the variations appearing in the land use may play a crucial role to maintain continuity of these areas. In this study, reduction of the negative interactions between urban settlement and urban land use with aquifer zone is investigated. In order to prevent aquifer zones from the harmful effects of the land use, Golbasi (Ankara) Special Environment Protection Area (SPA) was selected as sampling area. Environmental Arrangement Plan of Golbasi SPA, Protection of Golbasi SPA and aquifer areas, land use (both agricultural and urban) are formed material part of paper. A basic concept and technical process for the application of the GIS technique in the evaluating protection of aquifer areas of Golbasi SPA and relation between land uses are evaluated by GIS. The analysis of the evaluation model and data interpolation method for the model in GIS was done. Using Euclidean Distance Mapping (GIS) method, settlements were grouped according to the distance between each other and additional to that, areas, which should integrate through urbanization, were identified. Considering the aquifer zones present in the areas, which should not integrate with each other, a three-stage green area system was proposed. The most important point revealed in this study is that the protected areas suggested in Environmental Arrangement Plan of Golbasi overlap with the three-stage green areas formed by EDM technique. Moreover, the integration of the cities is prevented by this suggested study.