Intensifying human activity in the Yangtze River basin has substantially increased nutrient concentrations in the Yangtze River Estuary, leading to degradation of the coastal environment. Analysis of nutrient determinations published over the past 50 years reveals a gradual decreasing trend in the concentrations and fluxes of dissolved silicate (DSi). However, both dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphate (DIP) concentrations have increased significantly since the 1970s. The frequency of and area covered by red tide outbreaks have increased greatly during this period, mainly due to changes in nutrient supply ratios [i.e., N/P (DIN/DIP), N/Si (DIN/DSi), P/Si (DIP/DSi)]. A strong correlation was found between the riverine DIN fluxes and the estimated DIN inputs from the major N sources, particularly fertilizers and atmospheric deposition. The data provide a comprehensive assessment of nutrients in the Yangtze River basin and their ecological impacts and indicate a potentially significant influence of atmospheric deposition on DIN loadings and fluxes.