Natural resources degradation poses multiple challenges particularly to environmental and economic processes. It is usually difficult to identify the degree of degradation and the critical vulnerability values in the affected systems. Thus, among other tools, indices (composite indicators) may also describe these complex systems or phenomena. In this approach, the Water and Land Resources Degradation Index was applied to the fifth largest Mediterranean island, Crete, for the 1999–2014 period. The Water and Land Resources Degradation Index uses 11 water and soil resources related indicators: Aridity Index, Water Demand, Drought Impacts, Drought Resistance Water Resources Infrastructure, Land Use Intensity, Soil Parent Material, Plant Cover, Rainfall, Slope, and Soil Texture. The aim is to identify the sensitive areas to degradation due to anthropogenic interventions and natural processes, as well as their vulnerability status. The results for Crete Island indicate that prolonged water resources shortages due to low average precipitation values or high water demand (especially in the agricultural sector), may significantly affect Water and Land degradation processes. Hence, Water and Land Resources Degradation Index could serve as an extra tool to assist policymakers to improve their decisions to combat Natural Resources degradation.