As landscape disturbance and climate conspire to accelerate global environmental change towards unprecedented levels in the twenty-first century, the populated coastal regions of many countries are facing major threats to sustainability. Coastal water resources are particularly vulnerable in dry regions. In view of the expected severity of future environmental change in the Southern Mediterranean Region, the European Commission supported an integrated multidisciplinary project, MELMARINA, on monitoring and modelling coastal lagoons in Morocco, Tunisia and Egypt. This is a region where water management for people and for agriculture has been intense particularly during the twentieth century, yet long-term environmental monitoring and management of wetland ecosystems are under developed. Not only are biodiversity aspects at risk in coastal lagoons and wetlands but the goods and services that affect human welfare are also generally in decline. Co-ordinated hydro-ecological monitoring at key wetland lagoons was begun in 2003 with a view to establishing environmental baselines and calibrating site-specified hydro-ecological models. This article introduces the project and its results that range from lagoon typification and hydro-ecology to the application of hydro-ecological models. Detailed results and evaluations are presented in a linked series of themed scientific articles within this special issue. The present condition of the lagoons investigated essentially results from various hydrological modifications combined with eutrophication problems, yet all still remain valuable aquatic ecosystems. Adequate monitoring data are an essential part of reliable predictive modelling and, despite several data gaps, nutrient load reduction scenarios were undertaken to help target restoration aims. Implementation of aspects of the EU Water Framework Directive for achieving good ecological status of transitional waters is advocated. Nevertheless, as the twenty-first century advances the effects of global climate change are expected to amplify current stresses making intervention restoration and adaptation management even more imperative. Long-term sustainability depends upon detecting and measuring environmental change (long-term water quality and ecological quality) and incorporating the results into appropriate hydro-ecological models to facilitate the development of appropriate management initiatives.