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The Prespa Lake Basin is over 5 million years old – amongst the most ancient freshwater lakes in the world. The region of the lake is home to more than 2,000 species of fish, birds, mammals and plants and the largest breeding colony of Dalmatian pelicans in the world. Many of these species are unique and many are in danger of dying out if their habitat is not protected. Therefore the project aimed at improving Prespa Lake’s overall health, strengthen its resilience and ensure, in the long run, control of the eutrophication processes. This was achieved through the implementation of a set of comprehensive measures aimed at reducing the pressures from agriculture, forest land, polluted rivers, wastewaters and solid waste while creating sustainable monitoring and watershed management capacities at the local level. Aligned with the key principles of the EU Water Framework Directive and the underlying concept of the Integrated Water Resource Management, the ultimate impact of the project was to contribute to the improvement of the Prespa Lake’s ecological State and its resilience. The expected positive impacts include: 1) Improvement of the water and soil quality in the Prespa Lake watershed including control of erosion processes and reduction of the load sediment in the lake; 2) Reduction of the adverse apple farming processes; 3) Ensuring of flood control, retention and filtering of polluted tributaries and upgrade of the existing wastewater treatment technology for enhanced nutrient removal; 4) Wetlands restoration including the establishment of the Ezerani Nature Park; 5) Development of environmental infrastructure; 6) Improvement of waste management practices; 7) Sustainable watershed management practices at the local level; 8) Establishment of Lake Monitoring System and Management Service, and 9) Public awareness activities.