The growing Antwerp harbour on the left bank of the River Schelde has a considerable overlap with designated Birds and Habitats Directive areas (SPA and SAC). Harbour development projects threaten the favourable conservation status of the protected habitats and species. On the other hand the international conservation commitment hampers the harbour development. ‘Co-habitation’, the aim of the Flemish Government to maintain a balance between industrial and ecological needs is a key word in the present-day management of the region. The Deurganckdock case exemplifies possible problems and solutions for Natura 2000 in harbour development areas. Compliance with article 6 of the Habitats directive is the most complex issue. In this case it failed with respect to the assessment of adverse effects and several aspects of the compensation policy. Well defined conservation objectives and performance criteria are essential to the process and should be defined as soon as possible for any Natura 2000 site. Habitat creation/development as compensatory measure should start prior to and not simultaneously or after habitat destruction. Temporary compensations are no sustainable solutions and are only acceptable when an existing habitat is involved; temporary habitat creation is both an economic and ecological loss. Monitoring Natura 2000 sites is essential to successful adaptive management and the maintenance of a favourable conservation status, especially in highly dynamic areas such as harbour development areas.