In this special issue we examine the biogeochemical conditions and marine ecosystems in the major marginal seas of the western North Pacific Ocean, namely, the East China Sea, the Japan/East Sea to its north and the South China Sea to its south. They are all subject to strong climate forcing as well as anthropogenic impacts. On the one hand, continental margins in this region are bordered by the world's most densely populated coastal communities and receive tremendous amount of land-derived materials. On the other hand, the Kuroshio, the strong western boundary current of the North Pacific Ocean, which is modulated by climate oscillation, exerts strong influences over all three marginal seas. Because these continental margins sustain arguably some of the most productive marine ecosystems in the world, changes in these stressed ecosystems may threaten the livelihood of a large population of humans. This special issue reports the latest observations of the biogeochemical conditions and ecosystem functions in the three marginal seas. The studies exemplify the many faceted ecosystem functions and biogeochemical expressions, but they reveal only a few long-term trends mainly due to lack of sufficiently long records of well-designed observations. It is critical to develop and sustain time series observations in order to detect biogeochemical changes and ecosystem responses in continental margins and to attribute the causes for better management of the environment and resources in these marginal seas.