This research was undertaken to determine the concentrations of heavy metal ions in the surface water and sediment in water bodies that receive wastewater from the Dinh Tram and Pho Noi A industrial zones. The pollution status of the heavy metal ions and their potential ecological risks were evaluated by using the potential ecological risk index (RI) and risk assessment code (RAC). The results showed that some metal ions, namely Fe3+, Ni2+, and Pb2+, exceeded the allowed standards of QCVN 08:2023/BTNMT. The sediments were polluted by Zn2+, As2+, Cr6+, and Fe3+ at concentrations 2.4, 3.7, 1.9, and 2.0 times higher, respectively, than the QCVN 43:2017/BTNMT. The potential ecological risk indices for the heavy metal ions were in order as: (As2+) = 7.94 > (Cd2+) = 3.68 > (Cr6+) = 3.39 > (Pb2+) = 2.73 > (Cu2+) = 2.74 > (Zn2+) = 2.4 (T6 channel) and (As2+) = 11.1 > (Cd2+) = 7.74 > (Cu2+) = 2.64 > (Cr6+) = 2.31 > (Pb2+) = 1.9 > (Zn2+) = 0.87 (Bun River). The risk assessment code (RAC) ranged from 0.17 to 39.42 (T6 channel) and from 0.03 to 38.96 (Bun River). The RAC-based risk assessment results showed that both the T6 channel and Bun River presented a medium risk for Cd2+, a low risk for Mn2+, Zn2+, Cu2+, and Ni2+, and no risk for the remaining metals, Cr6+, Pb2+, As2+, and Fe3+. These results were caused by the differences in environmental quality assessments between using separate parameters versus biological risk assessments.