The Dutch government wants to expand Mainport Rotterdam, one of the largest ports in the world, by land reclamation in the North Sea. This may affect the Wadden Sea, a unique wetlands area protected by the European Bird and Habitat Directives. To assess the impact of the port extension on the Wadden Sea, an Appropriate Assessment procedure was carried out. We investigated how stakeholders' perceptions were dealt with and how knowledge was used in this decision-making process. Our findings form an argument for practitioners in marine and coastal management to choose a process-oriented approach to deal with complex issues.