The marginal seas of the western North Pacific Ocean are sensitive to climate variation, because they are adjacent to the western Pacific warm pool, and subject to the wind forcing of the East Asian monsoons, the buoyancy forcing of several large rivers, and the climate oscillation, such as ENSO. Continental margins in this region are bordered by the world’s most densely populated coastal communities and receive runoffs from highly populated large river basins. The intense anthropogenic pressure threatens diverse coastal marine ecosystems, as demonstrated by the four-fold increment of Changjiang nitrogen loading and rising atmospheric deposition of macro- and micronutrients in the past 30 years that possibly contribute to the increasing hypoxia in the East China Sea. Increasing frequencies of widespread flooding since the beginning of the 20th century, which is attributable to the accelerated hydrological cycle partly to changes in land-use, may also cause marked changes in coastal ecosystems. On the other hand, increasing impounding of freshwater for irrigation purposes may reduce riverine load of particles, dissolved silicate, altering discharge patterns, nutrient elemental ratios and phytoplankton community downstream. As continental margins sustain arguably the most productive ecosystems and most active biogeochemical processes in the earth system, the stressed ecosystems may threaten the livelihood of a large human population. Moreover, the altered biogeochemical cycles may cause unknown feedbacks that exacerbate the effects of climate change.