The Yi River, the second longest river in Shandong Province, China, flows through Linyi City and is fed by three tributary rivers, Beng River, Liuqing River, and Su River in the northeastern part of the city. In this study, we determined the concentrations of five heavy metals (Cr, Ni, Cu, Zn, and Pb) in water, sediment, and aquatic macrophyte samples collected from the junction of the four rivers and evaluated the potential ecological risk of heavy metal pollution. Most of the heavy metals in water were in low concentrations with the water quality index (WQI) below 1, suggesting low metal pollution. The sediments showed low heavy metal concentrations, suggesting a low ecological risk based on the potential ecological risk index (RI) and the geo-accumulation index (Igeo). The aquatic plant species Potamogeton crispus accumulated considerable amounts of heavy metals, which were closely related to the metal concentrations of the sediment. The plant species Salvinia natans also showed an excellent metal accumulation capability. Based on our results, the junction of the four rivers is only slightly polluted in terms of heavy metals, and the plant species P. crispus is a suitable bioindicator for sediment heavy metal pollution.