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The Wadden Academy is a compact organisation. Its major aims are to identify gaps in our knowledge of the Wadden Sea Region, to programme research and to disseminate the outcome. The research areas are: geoscience, ecology, society and cultural history, social and spatial economics, urban and rural planning and climate and water.

The Wadden Academy is funded by the Wadden Fund. The Wadden Academy specifically aims to achieve the fourth objective of the Wadden Fund: to develop a sustainable knowledge structure for the Wadden Sea Region.

The Board of the Wadden Academy consists of five part-time members. They are supported by an agency that is located in the House of the Wadden in Leeuwarden. The Wadden Academy regularly reports to a Supervisory Board. In 2016 a "Young Wadden Academy" was established. This step was taken to encourage researchers to study the Wadden Sea Region, preferably in multidisciplinary teams.