Southern Chile encompasses one of the most extensive fjord regions of the world, the Patagonia, currently exposed to natural and anthropogenic perturbations. These fjord ecosystems provide important services to humans, which have not been adequately measured and valued. As a consequence, ecosystem services are commonly ignored in public policy design and in the evaluation of development projects. Here we tackle questions that are highly relevant for the nation's development, namely (1) understanding fjord functioning, and (2) developing management strategies based on ecosystem services, in order to secure simultaneous and adequate use of these ecosystems which area influenced by ecological (e.g., biogeochemical) and productive (e.g., aquaculture, fisheries) processes. We also seek to strengthen the analysis of fjord ecosystem value from the economical (including coastal zoning), socio-cultural, institutional, and governmental points of view. In addition, the investigation of current and future effects of climate change on this large region offers a unique opportunity to understand the social and economic consequences of a global phenomenon at local to regional scales. Biogeochemical and socio-economic models will be used to simulate future scenarios under a gamut of management options.