Abstract The aim of this paper is to assess the possible contribution of an input–output model towards two of the basic principles of the sustainability strategy of integrated coastal zone management (ICZM) and Post-Normal Science. According to these principles, decision-support tools should offer a holistic perspective and handle high uncertainty. The difficulties in reaching sustainability are due partly to the prevailing use of “narrow-system-boundary” tools that are non-holistic. Consequently, they fail to capture important ecosystem services and ignore interdependencies between them. To comply with the basic principles, our method allows environmental assets to be evaluated in multiple units and integrates results from recent researches in natural sciences. Both enable coverage of interdependencies between ecosystem services. Thereby, we enlarge input–output modelling from the two conventional ecosystem services of sink and provisioning to the most vital ones: the supporting services. An application to the Seine estuary addresses the impacts of maritime transportation infrastructures on nursery habitats for commercial fish. The ecosystem services covered are life support and resource provisioning. Our results show that the restoration of a total of 73.7 km 2 of nursery areas over the period 2004–2015 would result in a stock of sole in 2015 that exceeds the “business as usual” scenario by 44.2% (uncertainty range: 35.9%–69.9%). In spite of high restoration costs, the negative macro-economic impact is very low. However, on the sector level, a trade-off results between nurseries and three economic sectors. The quantification of such trade-offs in our model is particularly useful to public participation in decision-making.