The Waddenacademie was founded in 2008 and functions as knowledge director for the Wadden area. The Waddenacademie is an independent foundation, the basic funding of which comes from the Wadden Fund. The research areas are: Geoscience & Climate, Ecology, Spatial Planning, Cultural History and Landscape, Economy, Nature & Law.

The Waddenacademie consists of five part-time portfolio holders. The portfolio holders are supported by an office located in the House for the Wadden in Leeuwarden. The Waddenacademie is assisted in terms of content by a Scientific Advisory Board, and is accountable to the Wadden Area Administrative Consultation (BOW) and the Supervisory Board of the Waddenacademie.