This study analyzes the water resources and ecological environment of the Yalu River estuary, which is expected to grow as a major logistics center in Northeast Asia. The Yalu River has supplied water and energy to North Korea and China, however it continues to cause water pollution in the estuary due to the eutrophication and the increasing heavy metal elements caused by waste water. The results of local water ecology studies and the similar overseas cases were analyzed in the study. After examining the environmental issues related to logistics, it identifies the main considerations for the construction of waterfront logistics centers and examines promising construction area. In the future, the Yalu River estuary should continue to grow into an environmentally friendly waterfront logistics center where the two countries cooperate each other. To this end, ICT-based twin smart city development can be considered, and the green logistics concept should be reflected by utilizing smart water technologies such as low-impact development (LID). As for the regional location of the logistics center, Dandong New District and Hwanggumpyong area, where the logistics is currently in operation or planned, can be considered as priority construction areas.