In order to fully understand the content of heavy metals in the sediments of the main water systems in Hunan Province and their potential ecological risks, 75 sediment samples were collected from five major water systems and analyzed. The correlation of the contents of various heavy metals in the sediments of the main water systems in Hunan Province was analyzed. Based on the sampling test results, the along the river distribution of heavy metals in the sediments of four rivers in Hunan Province was also analyzed. Through the content analysis of the Cd and Mn along the river, it was found that the change of Mn content along the river was similar to that of Cd, and the peak value of heavy metal content had an important relationship with the drainage enterprises, heavy pollution industrial parks and estuary siltation. The pollution degree and potential ecological risk were evaluated by the geo-accumulation index method, Nemerow index method and potential ecological risk index method. The results showed that the average contents of As, Cd, Cr, Cu, Mn, Pb and Zn were 32.87, 7.59, 78.09, 70.69, 1182.60, 85.64 and 482.44 mg/kg, respectively. The pollution of Xiangjiang River and Dongting Lake was relatively serious, and the content of heavy metals in the sediments was significantly higher than that of Zijiang, Yuanjiang and Lishui River. Correlation analysis showed that multiple heavy metals had the same pollution source. The evaluation results of the geoaccumulation index showed that the pollution level of Cd wss severe, level of Zn was moderate, level of Cu, Mn, and Pb were all mild, while the pollution levels of As and Cr were clean in the sediments of the main water systems in Hunan Province. The Nemero index evaluation results showed that, except for the light pollution of Cr, the other six heavy metal pollution in the sediments of the main water systems in Hunan Province were the severe levels. The potential ecological risk assessment results showed that the overall potential ecological risk of Hunan Province belonged to the medium level. The order of the potential ecological risk of each water system was Dongting Lake > Zijiang River > Xiangjiang River > Lishui River > Yuanjiang River. The potential ecological risk level of Cd was very severe and the level of other heavy metal elements were mild.