This paper compares the Yangtze Estuary in China and the Western Scheldt Estuary in The Netherlands by their morphodynamic and ecological systems, their engineering works and estuarine management issues, and the major challenges in studying them. Physically speaking, the two estuaries are very different. The Yangtze Estuary is much larger and much more influenced by the upstream river than the Western Scheldt. Yet, they also have a number of morphological and ecological features in common. Both estuaries have a multi-channel system and extensive intertidal flats and wetlands with ecologically valuable flora and fauna. These eco-morphological systems are influenced by similar societal developments and human activities. Examples of the latter are engineering works and dredging activities for improving and maintaining the navigation channels, and shoreline management activities including land reclamations and setbacks. The fundamental eco-morphological phenomena that remain to be analysed and understood are the same for the two estuaries and will be discussed in this paper.