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Soil is a considerable natural resource which is one of the cores of the natural ecosystems and is also under constant pressure. The sustainable environmental management of the natural resources necessitates the soil conservation and the systematic monitoring of the sensitive ecosystems, which are regularly exposed in desertification processes in the Mediterranean region. The Geographic Information Systems (GIS) in many cases function as a tool to the protected areas ecological management due to spatial modelling and quantitative methods. In the present study, in the catchment area of the artificial lake of Aoos Springs in the Northwest Greece, the Universal Soil Loss Equation (USLE) is implemented in order to assess the soil erosion risk. The combination between the derived soil erosion risk assessment and the Natura 2000 network, which is the ecological network of protected areas, provided an insightful view for any soil erosion impact on the natural habitat types. Preservation of the representative ecosystems is significant for the biodiversity worldwide and thus the sustainable ecological planning process for protected areas and soil conservation supply resilience in mitigating the environmental challenges of the climate change.