Dutch waters have been under construction ever since the nation exists and the resulting unique diversity of aquatic ecosystems has changed accordingly. Scientific research in the Netherlands has advanced approaches to re-create aquatic communities with remarkable successes. However, the development of aquatic ecosystems is not a simple and straightforward process regulated by existing water management and predicted by scientists. What did we learn from decades of interaction of water management and ecological science? Is there scope for capitalizing on the early success and increase predictive power? Is it possible to gear the development of science to a next generation experimental management of water systems? The challenges ahead follow from climatic and hydrologic changes, demands to improve urban ecology and human well-being and mitigate the risks of pollution. The Centre for Wetland Ecology has the ambition to support the process.