This paper outlines the implications of the Habitats Directive of the European Union for port extension projects. Descending from the ecosystem level to the species level it will also draw conclusions on what the successful and less successful elements in the practice of implementing the Habitats Directive requirements from a nature protection perspective are. The focus of the paper is on projects and plans for port extension in or in the proximity of designated sites and on species protection. On the basis of case studies of large ports in northwestern Europe, preliminary conclusions are formulated and recommendations for similar projects are presented.