The Salt Lake Specially Protected Area is a unique ecosystem for both agricultural activities and natural life in Turkey. In the present study, an attempt was made to develop a conceptual land use strategy and methodology, taking into account ecological factors for regional development in the Salt Lake Specially Protected Area. A detailed Geographic Information System (GIS) analysis was done to create a comprehensive database including land use, land suitability, and environmental factors (soil, climate, water quality, fertilizing status, and heavy metal and pesticide pollution). The results of the land suitability survey for agricultural use showed that, while 62.6% of the study area soils were classified as best and relatively good, about 15% were classified as problematic and restricted lands, only 22.2% of the study area soils were not suitable for agricultural uses. However, this is not enough to derive maximum benefit with minimum degradation. Therefore, environmental factors and ecological conditions were combined to support this aim and to protect the ecosystem. Excessive irrigation practices, fertilizer and pesticide application, and incorrect management practices all accelerate salinization and degradation. In addition to this, it was found that a multi-layer GIS analysis made it easy to develop a framework for optimum land use and could increase the production yield preserving the environmental conditions. Finally, alternative management and crop patterns were undertaken to sustain this unique ecosystem, considering water, soil, climate, land use characteristics, and to provide guidance for planners or decision makers.