Effective implementation of the new Greek governance system for Natura 2000 site protection and conservation relies on adopting innovative local participation methods. The remote and transboundary nature of Prespa Lakes presents unique challenges to environmental protection and efficient management of this protected area. Within the framework of the Horizon 2020 ARSINOE project, NECCA supervised three national workshops in the Greek part of the Prespa Lakes watershed, bringing together stakeholders from all relevant sectors that were selected based on their interest in and influence on the challenge of water management. These stakeholders mapped the complex interconnections between climate change; water management; and local issues like vegetation changes, population decline, and economic activities, revealing synergies as well as conflicts, eventually identifying innovation pathways for future climate resilience in Prespa and highlighting the importance of participatory governance for freshwater ecosystems. This paper explores the application of the System Innovation Approach and Living Labs methodology that produced mental maps, future visions, and identified innovations, thus fostering a comprehensive, multistakeholder approach to climate adaptation in water resources management. The future goal is to examine the transferability of experience and insights gained in Prespa to other Greek Protected Areas with similar ecosystem characteristics and challenges.