The coupling effect of damming and urbanization on nutrient dynamics renders the aquatic environment sensitive and vulnerable, posing a significant global concern. However, the role of damming as a source or sink of nutrients remains uncertain. In this study, river water samples were collected in the Three Gorges Reservoir (TGR), which is recognized as the world's largest hydropower engineering. By integrating solute chemistry and flux budget modeling, the status, source, and transformation of riverine nutrients were revealed, and the interplay between water storage and human inputs on TGR nutrient dynamics was discussed. The concentrations of TDN and DSi were 100.2 ± 46.1 μmol/L and 115.7 ± 14.1 μmol/L, respectively. NO 3 − −N (77.9 ± 64.1 μmol/L) was the main species of TDN, with NH 4 + −N and dissolved organic nitrogen accounting for only 2.5 and 19.7%, respectively. DSi was attributed to silicate weathering, while riverine NO 3 − −N exhibited a significant influence from anthropogenic inputs. About 71.7% of NH 4 + −N was retained or converted to NO 3 − −N by nitration along the river. Evidence from the significant correlation (p < 0.05) between NO 3 − −N/NH 4 + −N and d-excess suggests that the evaporation process accelerated by damming promotes nitrification. Through the anthropogenic net nitrogen input model, atmospheric nitrogen deposition was the primary factor affecting nitrogen flux in TGR river water, highlighting the critical impact of urbanization. The estimated contribution fluxes of stored nitrogen from 1997 to 2020 exhibited a limited contribution ratio and decrease yearly, supporting that water level rise from damming promotes the release of stored nitrogen. This study enhances the comprehension of the anthropogenic impacts on the nutrient biogeochemical cycle in damming rivers, providing enlightenment for environmental health management in large reservoirs.