In the present study, δ(15)N and δ(18)O-NO(3)(-) values, as well as concentrations of some major ion tracers were determined in seasonal water samples from Taihu Lake and major watersheds to investigate the temporal and spatial variations of nitrate sources and assess the underlying nitrogen (N) biogeochemistry process. The results lead to the conclusion that the nitrate concentrations in Taihu Lake are lower in summer than that in winter due to the dilution effect of wet deposition. In winter, sewage and manure were the primary nitrate sources in major inflow rivers and North Taihu Lake (NTL), while nitrate sources in East Taihu Lake (ETL) probably derived from soil organic N. In summer, atmospheric deposition and sewage/manure inputs appear to play an important role in controlling the distribution of nitrates in the whole lake. The δ(18)O-NO(3)(-) values suggest that the nitrate produced from microbial nitrification is another major nitrate source during both winter and summer months. The variations in isotopic values in nitrate suggest denitrification enriched the heavier isotopes of nitrate in NTL in winter and in ETL in summer.