Nitrogen (N) and phosphorus (P) flows from land to sea in the Yangtze River basin were simulated for the period 1900–2010, by combining models for hydrology, nutrient input to surface water, and an in-stream retention. This study reveals that the basin-wide nutrient budget, delivery to surface water, and in-stream retention increased during this period. Since 2004, the Three Gorges Reservoir has contributed 5% and 7% of N and P basin-wide retention, respectively. With the dramatic rise in nutrient delivery, even this additional retention was insufficient to prevent an increase of riverine export from 337 Gg N yr−1 and 58 Gg P yr−1 (N:P molar ratio = 13) to 5896 Gg N yr−1 and 381 Gg P yr−1 (N:P molar ratio = 35) to the East China Sea and Yellow Sea (ECSYS). The midstream and upstream subbasins dominate the N and P exports to the ECSYS, respectively, due to various human activities along the river. Our spatially explicit nutrient source allocation can aid in the strategic targeting of nutrient reduction policies. We posit that these should focus on improving the agricultural fertilizer and manure use efficiency in the upstream and midstream and better urban wastewater management in the downstream subbasin. Display omitted •The spatiotemporal changes of N and P sources in YRB were simulated for 1900–2010.•Results indicate 17-fold increase in N export (7-fold increase in P) for 1900–2010.•The impact of the TGR on the whole-basin nutrient retention was limited.•The TGR retention implies an increasing risk of HABs within the reservoir itself.•The ratio of N/P exporting to the coast increased from 13 in 1900 to 35 in 2010.