Nutrient element cycling in the Tibetan Plateau, the highest and largest plateau in the world, is sensitive to anthropogenic disturbances and climate change. Studying the spatiotemporal dynamics of reactive nitrogen (N) – predominantly in the form of nitrate (NO3–) – in the plateau is crucial to understand the regional and global N cycles and their feedbacks with climate change. We conducted the first weekly frequency hydro-geochemical monitoring (i.e., discharge, water chemistry, and multiple isotopes) from the upper to the lower reaches of the Yarlung Tsangpo River, the largest river in the plateau, in pronounced wet/dry cycles to reveal the biogeochemical transformations and fluvial fluxes of NO3– response to hydrologic condition. Relative stable NO3– concentration and significant linear correlations between the fluvial NO3– fluxes and the discharge were observed, suggesting that a significant potential NO3– source counterbalanced the diluting effects during the rainy season. The negative correlations between δ15N-NO3− and discharge/NO3− fluxes suggested that the increasing NO3− flux respond to the increasing discharge was mainly from water leaching of 15N-depleted soil sources, rather than 15N-enriched sewage. The isotopic mixing model calculation showed that NO3– fluxes were largely generated in the relatively densely populated middle reaches (56%), of which 74% were from soil sources. The fluxes of the soil sources showed large seasonal variation and peaked in August, with hydrological condition as the primary driver. Based on the critical findings, we put forward a NO3− export conceptual model that integrated anthropogenic and climatic forcings and classified NO3– export mechanisms in river basins into transport-limited and generation-limited regimes. In a transport-limited regime that characterized most river basins in the Tibetan Plateau, fluvial NO3− flux presented a linearly relationship in response to runoff variation. In contrast, in a generation-limited regime, the flux would be largely dependent on the thermodynamic of nitrification.