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Semi-arid Mediterranean regions are highly susceptible to desertification processes which can reduce the benefits that people obtain from healthy ecosystems and thus threaten human wellbeing. The European Union Biodiversity Strategy to 2020 recognizes the need to incorporate ecosystem services into land-use management, conservation, and restoration actions. The inclusion of ecosystem services into restoration actions and plans is an emerging area of research, and there are few documented approaches and guidelines on how to undertake such an exercise. This paper responds to this need, and we demonstrate an approach for identifying both key ecosystem services provisioning areas and the spatial relationship between ecological processes and services. A degraded semi-arid Mediterranean river basin in north east Spain was used as a case study area. We show that the quantification and mapping of services are the first step required for both optimizing and targeting of specific local areas for restoration. Additionally, we provide guidelines for restoration planning at a watershed scale; establishing priorities for improving the delivery of ecosystem services at this scale; and prioritizing the sub-watersheds for restoration based on their potential for delivering a combination of key ecosystem services for the entire basin.