Over the last several decades, the Changjiang (Yangtze River) watersheds has suffered from an acceleration of economic activities and changing land-use patterns. Monitoring programs at downstream hydrological stations and data from field campaigns have shown that these changes have caused an increase in the loss of chemical elements (e.g., plant nutrients such as N, P, and Si) from catchment areas and changes in pollutant discharges (e.g., trace elements). Changes in plant nutrients and trace elements in the river have altered the partitioning of chemical species between water and solid phases (e.g., total suspended matter) in aquatic systems, in both freshwater and marine environments. Irreversible element partitioning in rivers and coastal waters can affect the bioavailability of chemical species in adjacent marine environments, which can in turn impact ecosystem structure and functioning. In the East China Sea, the continual increase in plant nutrient fluxes from land sources, such as the Changjiang, has caused eutrophication in surface waters of the coastal environment. The degradation of organic matter, either allochthonous or autochthonous in origin or both, has fueled heterotrophic processes that induce the seasonal depletion of dissolved oxygen (DO) and even hypoxia in the Changjiang Estuary and the inner shelf of the East China Sea. Based on observational hydrography and chemistry data, a box model approach is used in this study to describe the plant nutrient and trace element budgets. The results illustrate that incursion across the shelf break of the western boundary current system (i.e., Kuroshio) has a significant influence on the inventory and residence time of chemical elements such as plant nutrients on the East China Sea Shelf.