We investigated the occurrence of cadmium (Cd), copper (Cu), chromium (Cr), nickel (Ni), lead (Pb), Znic (Zn), iron (Fe), manganese (Mn), and magnesium (Mg) in sediments, as well as in related soils and aquatic plants in the Liangtan River, a typical secondary anabranch of the Yangtze River in the Three Gorges Reservoir Region (TGRR) of China. We found that sediments accumulated more metals than soils and aquatic plants. Concentrations of the nine metals in sediments and soils followed the same sequence, while their concentrations in aquatic plants followed a different sequence. Potential adverse effects of contaminated sediments on benthic fauna were evaluated, and the results showed that the toxic effect on benthic organisms followed the sequence Zn > Ni > Cr > Cu > Cd > Pb. The potential ecological risk index analysis indicated that Cd in sediments had considerable ecological risk, whereas Cr, Cu, Zn, Ni, and Pb had low ecological risk. The potential ecological risk index (RI) of the heavy metals in sediments of the Liangtan River was 174.9, indicating moderate ecological risk. The transfer factor trend of metals for aquatic plants showed that Cd and Ni had the most and least accumulation, respectively. For Cu, Cd, Mg, Pb, and Cr, a significant positive correlation of the metal concentrations was observed between sediments and soils, but no correlations (excluding Cr) were detected between sediments and aquatic plants. Our study indicated that anthropogenic input may be the primary source of metal contamination in the Liangtan River, and that Zn and Cd pollution in the Liangtan River should be further explored.