In this paper, we propose a methodological approach to study interactions between economic activities and the environment. The approach consists in integrating intermediate ecosystem services (mainly supporting and regulating services) inside an input-output model. This category of services conditions the existence of all other ecosystem services needed to ensure human life and activities. Our methodological approach is tested on a real case study, the one of restoration of nursery habitats in the Seine estuary. The simulation of restoration scenarios shows that in spite of very high implementation costs, macroeconomic impacts are negligible. Contrarily, at sectorial scale, the impact of costs is significant for three sectors. At ecological levels, impacts are positive and lead to an important increase of fish stocks generated by natural habitats in the estuary. Due to its capacity to quantify trade-offs between various uses of ecosystem services, the methodological approach developed in this paper is a promising tool for participative decision processes.