Typical country WLFZ in Zhongxian located in the core region of the Three Gorges Reservoir was chosen as research subject in this study. In July 2012, sediment samples of WLFZ were collected after dam water level dropped. Heavy metals were analyzed for sediment potential risk assessment and then applied for sources analysis in this area, which supplied basic data for non-point pollutants control. The results showed that As, Cd, Co, Cr, Cu, Mn, Ni, Pb and Zn ranged in 155-160 m:5.17-14.81, 0.06-0.57, 8.55-20.56, 62.79-93.04, 15.38-60.97, 425.72-782.32, 21.34-48.5, 23.03-43.39 and 57.78-130.10 mg x kg(-1), and 170-175 m: 7.05-12.57, 0.17-0.33, 10.71-18.89, 65.22-92.89, 18.89-42.91, 74.06-774.41, 22.47-42.49, 24.17-29.23, 55.67-103.18 mg x kg(-1), respectively. Index of geo-accumulation (Igeo) suggested the accumulation orders were Cd > Co > Mn > As > Cu > Pb > Zn in 155-160m WLFZ and Co > Mn > Cd > As in 170-175 m WLFZ. Sediment pollution index (SPI) showed that sediments in 155-160 m WLFZ had higher potential risk than that of 170-175 m with the highest risk appeared in 155-166 m WLFZ site located downstream of Zhongxian. In 155-160 m WLFZ, Cr, Cu, Pb and Zn were mainly originated from natural resources, while As, Ni, Cd, Co and Mn were possibly sourced from upland water. In contrast, in 170-175 m WLFZ, Cr, Ni, Pb and Zn in the sediment came from natural resources, while Cd, As, Co, Mn and Cu were probably rooted from both agricultural non-point source and upland water.