The Wadden Sea and the IJssel- and Markermeer were once part of the single estuary of the Zuiderzee, but have become units since closure of the Afsluitdijk in 1932. Both ecosystems continue to be of great importance as habitat for aquatic organisms, yet they also face many challenges for the conservation of plants, fish and birds. In this CWE symposium we investigate the main drivers of the functioning of these large marine and freshwater ecosystems and pay ample attention to the many new initiatives to restore and improve the quality of nature from Wadden Sea to Marker Wadden.