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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 & climate, ecology, cultural history, economy, nature & law.

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 and a Scientific Advisory 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.