The spatial distribution of the sediment nitrogen in ten typical estuaries of Lake Taihu was determined. A simple quantitative estimation model and principal component analysis (PCA) method were applied to find the source and major factors of estuarine sediment nitrogen loading. The average concentrations of total nitrogen (TN), organic nitrogen (Org-N), ammonium nitrogen and nitrate-nitrogen in the sediments of the ten estuaries were 1315.5, 1220.1, 82.53 and 6.45 mg/kg, with the organic fraction dominating. Results showed a significant difference for the TN concentration in sediments of different estuaries, which was mainly caused by geographical location, land use type and vegetation restoration measures. An important result was that sediment nitrogen in 80% of the estuaries was mainly originated from autochthonous algae and presettled organic matter, although there has been continuous pollution input from inflow rivers. The source estimation results found that the autochthonous aquaculture excretion, algae and hydrophyte debris and buried biodetritus accounted for 58.9% of the total nitrogen loading, which dominated the nitrogen sources compared with the pollution input. In addition, the PCA method was used to find that phosphorus loading and redox conditions were the major limiting factors affecting the distribution of inorganic and , respectively.