Ecologists and social scientists have only recently realized that in order to fulfil the requirements for sustainable development, human beings have to be explicitly incorporated as structural components of ecosystems. Indeed, the clear distinction between natural and managed ecosystems is slowly fading-away, leaving us with the task of re-writing ecological theory in order to incorporate anthropogenic pressure. New concepts, necessary to understand these eco-social systems, will be assessed in the ECOMANAGE project, based on a modular approach to ecosystem modelling. This approach comprises physical and ecological models for computing transport and biological activity in the aquatic system. Anthropogenic influence on the drainage basins, determined by satellite data and models for ground and surface waters, will be translated through boundary fluxes to the aquatic system. These tools will cover problems and key issues identified in study areas. Environmental state and impacts will be translated into indexes to be incorporated on a spatial decision support system backed in the DIPSR decision framework. Local stakeholders will help establishing study scenarios and indexes for social-economic analyses. The project will focus on three different coastal zones. These sites include an estuary with mangroves in Brazil, a fiord in Chile and a large estuary with wide intertidal areas in Argentina. These systems host very important economic activities (including two important ports) and have been studied by major universities and/or research institutes in the respective countries.