Field surveys were carried out from January 2007 to December 2008 to investigate seasonal variations of dissolved inorganic nitrogen (DIN) and phosphorus (DIP) transported to the Linjiang Bay of the Three Gorges Reservoir, China. The results revealed that both DIN and DIP exhibited large seasonal variability. DIN (dominated by NH4-N) concentrations were drastically higher in the dry season than those in the rainy season, and the same seasonal patterns of DIP concentrations and DIN and DIP fluxes were observed but inverse to that of DIN concentrations. The interannual variation in DIN fluxes descended by 28.2% from 2007 to 2008, while DIP fluxes increased by 40.9%, which were closely constant with interannual changes in DIN and DIP concentrations, respectively. The study indicated that nutrient fluxes (DIN and DIP) were strongly correlated with both nutrient concentrations and river discharge, and the Linjiang Bay received approximately 3,416×10(3) kg DIN and 324×10(3) kg DIP every year. In addition, DIN mainly originated from point sources, but DIP originated from non-point sources. It is shown that to control point source pollution is the most effective step for water quality improvement and reducing nutrient loading inputs in the Linjiang Bay.