The Natura 2000 (N2K) network is a key conservation instrument in Europe, despite its many limitations concerning the efficacy in covering and adequately safeguarding the marine environment, mainly due to missing coordinated Governance and Management Systems (GMS). In this study, we present and discuss the main benefits, which could be provided by Marine Ecological Observatories (MEOs) to support N2K marine network implementation and related GMS. The conceptual design of the ecological observatory ECOAdS, under development in the framework of the Interreg Italy-Croatia project ECOSS, is described. ECOAdS, which focuses on marine N2K sites under jurisdiction of Italy and Croatia, is a first operative pilot proposal of MEO for the Adriatic Sea. It represents an opportunity to build a common knowledge and monitoring framework and shared data management practices at the transnational level, overcoming the N2K site fragmentation. The main challenges that ECOAdS should face in its implementation are discussed, with emphasis on the integration of the marine connectivity aspects and on the adoption of adaptive and participative GMS to address the main conservation issues in the area.