For an integrated management of estuarine socio-ecological systems it is necessary to adopt an ecosystem approach and to elaborate proposals adapted to the social, administrative and ecological characteristics.An appropriate spatial scale approach should include interrelated and mutually interfering elements. Managing uses and occupation in a sustainable way involves managing natural resources and ecosystems, establishing proposals consistent with the concept of sustainability and that can be successful in a long-term projection. Thus, the transversal concept of ecosystem services and ecosystem-based management (EBM) responds to this need, especially when applied to an international and cross-border estuary such as the Guadiana River.The present research delimits and diagnoses the socio-ecological elements and the relations among economic and social sectors, environment and administrative and political components. It aims to justify the priority and strategic elements needed for manage the system in the European Union Framework. Protected areas and their management were also analyzed as articulators of the resources and territory management. The results of the analysis demonstrated the need to delimit the management area. For the Guadiana estuary, it goes up to 1644km2 on land and 4 kilometers seawards.The main instruments and opportunities presented in the case of the Guadiana river estuary, such as land-use management plan and especially the protected areas management plan, suggest a well-defined scenario and an integrated and ecosystem-based approach to its management. The main sectors considered (tourism, farming, navigation, fishing and aquaculture), their relationship with the environment, as well as the European Union framework, strengthen the proposal of an integrated management of the estuarine socio-ecological system based on existing opportunities and considering socio-environmental characteristics and initiatives and interests present in the system.