In this research, the dilemmas between protection and land-usage that are conflicted in legally protected natural sites in Turkey, and the impact of the legal obstacles together with court orders on environmental components and the nature have been examined. The original aspect of the research is integration of the protected natural zones and the legal decisions that were taken on the sites via Geographical Information System (GIS) by taking social structure and legal procedures into the account, and also determining the impact they have through presentation of visual and analytical perspectives. The research areas chosen were the villages of Ciceklikoy and Yaka, which are classified as first grade natural zones by the protection laws of Turkey in 1999, and became subject to dispute through many individual court appeals. During the legal process, the official complains were examined within the frame of the current law and legislations, and a variety of decisions were taken determining the land-use on existing protection zones. The results obtained were scrutinized within the frame of technical and legal perspective; both during the determination of protection grades and afterwards, during structuring sustainable and well-balanced relation of the protection and the usage, which is also available for development; therefore, suggestions were made accordingly, both for the afore-mentioned problems and for the complaints caused by employment loss. The importance of GIS application during planning and conflict resolution for protected natural sites was emphasized.