Over the last decades, the People’s Republic of China experience large economic development, which have led to severe shortages of usable land. To counteract this, the Chinese central government promoted the development of coastal provinces by reclaiming large sections of coastal zones. One of these regions is Nantong Binhai Park or Tongzhou Bay on the Jiangsu coast. This region is characterized with large intertidal mudflats and tidal channels and has a high potential for the development of agri-aquaculture as well as the construction of a deep-sea port. However, these intertidal mudflats are a vital part of ecosystems and support numerous species, such as several endangered migratory shorebirds within the East Asian–Australasian Flyway. Acknowledging the importance of both port development and existing endangered ecosystems, a more integrated coastal design is needed. Possible solution could be found through the Building with Nature approach, in which natural processes and ecological needs are included in the design. This requires a good understanding of the governing processes as well as the requirements from society, ecology and engineering perspectives. In this thesis, a preliminary study was performed into a more sustainable alternative for the planned Tongzhou Bay Port, in which a basic connection was made between engineering and ecological point of view. A hydro-morphodynamic numerical model was made available and further developed for the modelling of the governing processes in the development of the intertidal mudflats at Tongzhou Bay. The model showed satisfactory results with respect to observations and net flow and transport features were closer analyzed. The different ecosystem types at Tongzhou Bay were quantified with ecotope classification and further validated with satellite-tracked data of two endangered shorebird species. Based on this validation, high-value ecotopes were determined based on these species and was used as an indication for the performance of alternative port configurations with respect to ecology. With a better understanding of the governing processes for the development of the intertidal mudflats and ecotopes, a series of alternative port designs were conceived through several design cycle iterations. Guiding principles were the preservation of high-value ecotopes, the enhancement of these area’s development and the potential area created for future port development by each variant. Results showed that by understanding natural transport and siltation patterns, not only could alternative port configurations lead to the preservation of existing high-value ecotopes, but a stronger development of these areas with respect to the natural development could be realized as well. The preliminary results of this thesis show the potential of more sustainable alternative port designs through the Building-with-Nature principle, in creating benefits for both economic and ecological development of Tongzhou Bay.