Estuaries are among the most biologically productive and intensively used marine areas in the world. Their diversity and the number of interrelationships and conflicts of use make their sustainable management difficult. In the face of climate change, however, “business as usual” scenarios are becoming less and less viable. This is particularly true for the Elbe estuary of the North Sea, which is the lifeline of the Hamburg metropolitan region and the Port of Hamburg. Although scientists and stakeholders recognise the need for action in the face of high environmental and economic costs and increasing flood risks, there is no widely accepted strategy for a sustainable, resilient future for the estuary. Based on stakeholder workshops and publications, as well as the scientific literature, we have analysed several adaptation scenarios. We adopt the strategy of adapting the estuary geometry and use a numerical model for cross-sectoral analysis of system responses.