Abstract: The seasonal variations of concentrations and fluxes of dissolved inorganic nitrogen (DIN), activated phosphate (PO₄-P), and active silicate (SiO₃-Si) in the Yangtze River (YZR) were investigated bimonthly during 2011~2014.The annual variations of the DIN, PO₄-P, and SiO₃-Si fluxes as well as their effects on the nutrient concentrations and ratios in the Yangtze Estuary (YZE) were discussed.The DIN concentrations were higher in summer and autumn than in winter and spring, while the PO₄-P concentrations were higher in autumn and winter than in spring and summer.The SiO₃-Si concentrations were significantly related to the total suspended particulate matter and showed no obvious seasonal variation.The seasonal fluxes of DIN and SiO₃-Si followed the runoff variation and were higher in summer than in winter, while the PO₄-P fluxes were higher in autumn than in winter.Historic records from 1960s to 2010s showed a 9.5-fold and 3.6-fold increase in the DIN and PO₄-P fluxes and a 0.6-fold decrease in the SiO₃-Si fluxes.Accordingly, the average annual concentrations of DIN and PO₄-P in the YZE increased by 4.5 and 0.8 times, respectively, while that of the SiO₃-Si decreased by 0.6 times, meanwhile, the ratio of N/P increased by 2 times, and the ratio of Si/N and Si/P decreased by 0.9 and 0.8 times, respectively.The variations of nutrient input by YZR might be attributing to an increase in red tide scale and a decrease in the proportion of diatoms in the YZE in the past 60 years.