River-sea transition plays a key role in global geochemical cycles. This study proposed a Section-Segmented Method (SSM) to determine the nutrient discharge from the Yangtze River to the East China Sea (ECS), against the high-density data of water flux and nutrient by the combination of artificial and tele-control monitoring. During 2012–2016, the nutrient delivery exhibited a pronounced inter annual variation, and the mean fluxes of TN and TP were respectively 1.69 Tg/yr and 0.11 Tg/yr. The year of 2016 was characterized by the highest level, with the loads of 2.00 Tg and 0.115 Tg for TN and TP, respectively. The river transported the maximum monthly flux in July, yielding 270.97 Gg and 15.62 Gg for TN and TP, respectively. The 5-year mean daily TN and TP flux were respectively 4.62 Gg and 0.27 Gg. The daily nutrient flux showed a pronounced and positive relationship with net water flux, but due to the different input modes of N and P, TP flux displayed a higher dispersion than TN. The degrees influenced by the South-to-North Water Transfer Project (SNWTP) in the nutrient delivery were stably maintained at the level of 2.50% and 2.36% for TN and TP, respectively, whereas the Three Gorges Dam (TGD) just harnessed 0.60% and 0.26%.