Vegetated drainage ditches (ecological drainage ditches, EDD) are commonly used for the treatment of nutrients, suspended solids, and pesticides, from agricultural lands and aquaculture effluent. However, their effectiveness to remove heavy metals/metalloids (HM/Ms) and fate remains largely unexplored. In addition, there exists some uncertainty concerning the performance of the EDD in treating HM/Ms. This study presents a thorough assessment on the removal efficiencies of HM/Ms and identifies the parameters affecting the HM/Ms removal process in the EDD receiving primary domestic sewage for 13 years. The mean concentrations of the studied HM/Ms in sediments were lower than those reported in the aquatic ecosystems affected by coal-mine drainage and industrial wastewaters. The results also showed that the concentrations of the selected HM/Ms in ditch sediment were generally far higher than the soil background values of Sichuan basin. Concentrations of all the studied HM/Ms and nutrients in water entering the EDD were significantly higher than the effluent. The annual mean removal efficiencies of Ni, Cu, Cr, Zn, Cd, Pb, As, Fe, Al, Mn, N, and P in the ecological drainage ditch were 50.6, 56.1, 63.3, 79.3, 67.5, 80.1, 60.3, 52.6, 19.8, 24.3, 72.0, and 59.7%, respectively. The study also displayed that dissolved oxygen levels at the outlet were significantly (p < 0.001) higher after passing into the EDD system. The pH was kept at neutral or alkaline. Removal of HM/Ms and nutrients was seasonal, generally peaking in the growing season. Sedimentation was the major mechanism removing HM/Ms within the EDD system. EDD was found to possess a favorable influence at mitigating HM/Ms and nutrients in situ and can be successfully utilized to resolve this type of environmental pollution.