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In recent years, the competition of uses for scarce and highly valuable natural resources, and the frequency and severity of natural and technological disasters have increased, and this trend is likely to worsen in the years to come. In the Mediterranean area, especially in its Eastern part, the high human exploitation driven by different economic sectors and interests is resulting in intensive use of the land and its resources. Tourism intensification, rapid growth of urban settlement and related sprawl, movement and displacement of populations, rural abandonment, and adoption of different agricultural techniques are profoundly and rapidly changing the landscape character of the East Mediterranean. In view of the risks to cultural and natural heritage, a Landscape Risk Assessment Model (LRA) and Decision Support System (LDSS) were developed through the MedScapes-ENPI project. This paper reports the experience conducted at the Landscape Design and Ecosystem Management Department (LDEM) in the American University of Beirut (AUB) in developing the two tools, LRA and LDSS. It aims to provide insight into the methodology designed and tested during the length of the project to take into account the protection of landscapes of particular interest as well as the rational planning of all the landscapes with special emphasis on the use of natural resources. The assessment was applied in the study area of each partner country of the ENPI project, allowing for a better understanding of the implications in land-use and conservation decision-making.