The blue economy is recognized as a viable approach for both conservation of environmental capital and sustainable economic growth. All aquatic ecosystems, both freshwater and marine, should be included under the umbrella term “blue economy.” Freshwater habitats are among the most vulnerable areas in the world, even though they provide many important ecosystem services (ES) to humans. In this paper we study the Prespa lakes Basin on the Balkan Peninsula in Southeast Europe. The Prespa lakes are a system of two lakes, the Macro (Megali, Large) Prespa lake and the Micro (Mikri, Small) Prespa lake. The Prespa lakes basin is a unique natural area of great ecological, geomorphological, and cultural importance. Prespa lakes provide a wide range of provisioning, regulation and maintenance, and cultural ecosystem services, including the supply of food and water, the mediation of contaminants, and the climate regulation, in addition to physical and intellectual benefits. The supply of ecosystem services from the Prespa lakes basin is at risk due to the ecological damage caused by human activity. The restoration and protection of the terrestrial and aquatic environment is crucial to ensure the long-term viability of future generations.