Comprehensively characterizing and assessing the sediment quality in freshwater ecosystems based on the condition of the nutrients in eastern China was urgent. The distribution and concentration of nutrients were investigated; meanwhile, sediment quality guidelines (SQGs), organic pollution index (OPI), and organic nitrogen index (ONI) were used to assess the sediment quality. Total phosphorus (TP), total nitrogen (TN), and total sulfur (TS) concentrations in sediment samples were 48.4, 72.5, and 89.5% higher than the soil background value, respectively. In terms of the Ontario SQGs, 41.8 and 74.7% of sediment samples were severely polluted by TP and TN, respectively. The Haihe, Yangtze, and Pearl River Basins were much more severely contaminated than other basins. TN pollution was much more severe than TP pollution in all basins. The Haihe, Huaihe, and Pearl River Basins were seriously contaminated according to the OPI and ONI. On temporal scale, the TP and TN significantly increased since 1980s because of the social and economic development in eastern China. For most severely contaminated basins, TN contamination was higher than TP contamination, and concentrations of TN and TP continuously increased from 2007 to 2016, which ranged from 2.06 to 2.51 g/kg, and 1.02 to 1.22 g/kg, respectively, in the Haihe River Basin. This trend will continue without effective control. The freshwater sediment quality in eastern China revealed urgent attention.