The present study assessed the export of inorganic carbon, nitrogen, and phosphorus within a large agricultural basin in arid northwestern China. Groundwater of various depths and river water along a 160 km reach were sampled during contrasting flow conditions. Dissolved inorganic carbon (DIC) concentrations and δ¹³C-DIC values indicate that lithogenic carbonate weathering was the main source of DIC in the basin. Discharge played an important role in regulating the amount and flowpath of nutrients mobilized from soils to the river. Ammonium was mobilized mostly by storm flows whereas the other nutrients were exported through both storm and groundwater flows. Hydrological events, occurring on only about 10% of the days for a year, were responsible for more than 40% of annual nutrient exports. Shallow groundwater was an important source of DIC and nitrate in river water within the alluvial plain, where groundwater discharges regulated their longitudinal variability along the river. According to a mixing model using δ¹³C-DIC and chloride, groundwater comprised 9–34% and 39–60% of river water at high discharge and baseflow, respectively. Together, our data highlight the importance of reducing storm runoffs and monitoring nutrient pollution within this large basin.