The fast economic development of the People's Republic of China has created an increasing demand for usable land, resulting in large-scale land reclamations along the coastal zone. One of these regions is Tongzhou Bay (Jiangsu coast), a region characterized by large intertidal mudflats and deep tidal channels with potential for the development of agri-aquaculture and the construction of a deep-sea port. However, these intertidal mudflats also provide vital ecosystem services and support many wildlife species, including several endangered migratory shorebirds within the East Asian-Australasian Flyway. With increasing realization of the importance of maintaining such ecological values, a more integrated coastal development strategy is needed. This study aims to develop a sustainable integrated design for the Tongzhou Bay port, following a "Building with Nature" approach. We use a morphodynamic model to compute habitat suitability for two shorebird species (Great Knot Calidris tenuirostris and Bar-tailed Godwit Limosa lapponica). Several port configurations were developed on the basis of three design criteria: (1) create area for future port development, whilst (2) preserving existing high-value ecotopes for shorebirds and (3) enhance the natural accretion rate of such ecotopes. Simulation results showed a clear difference in siltation patterns, preservation and enhancement of preferred ecotopes. This work therefore demonstrates the potential and importance of morphological and habitat suitability modelling when designing large-scale reclamations and port constructions, especially in dynamic areas such as Tongzhou Bay.