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Deteriorating urban water quality has attracted considerable attention in China. We investigated the contamination levels and distribution of heavy metals (As, Cd, Cu, Ni, Pb, and Zn) in Yuxi River water and sediments, and assessed the heavy metal accumulation capability of five species of submerged macrophytes: Vallisneria natans (Lour.) Hara, Potamogeton pectinatus L., Hydrilla verticillata (L. f.) Royle, Myriophyllum spicatum L., and Potamogeton crispus L. Samples were collected from upstream and downstream locations in different season. The results showed that the levels of heavy metals in the downstream areas were higher than in the upstream areas. Heavy metal concentrations in the river water during the dry seasons were higher than those during the rainy seasons, and the opposite results appeared in sediments and submerged macrophytes. In general, the river was slightly contaminated by heavy metals, and the concentrations of Pb and Ni in this river should serve as a warning, while Cd and Zn pollution in the sediments desperately needs to be removed. Furthermore, Potamogeton pectinatus L. showed a higher accumulation capacity for these metals among the five native submerged macrophytes and could be defined as a hyperaccumulator for Cd. Therefore, the potential use of native aquatic plants in contaminated rivers is worth further exploration.