This study was conducted to investigate the retention and distribution of Cu, Pb, Cr, and Zn in a hybrid constructed wetland (CW) that consists of both vertical baffled flow wetlands (VBFWs) and horizontal subsurface flow wetlands (HSSFs) with unique flow regimes and oxygen distribution. The heavy metal concentrations in water, sediments, and plant tissues in the hybrid CW were analysed. The removal of heavy metals from the water stream in the monitoring period was not statistically significant. Metal concentrations in the sediments generally decreased along the wastewater treatment process. The reductive anaerobic condition in the VBFW may promote the sulphate reduction and form highly insoluble Cu, Pb, and Zn sulphides, resulting in the higher concentration of the bivalent cations in the VBFW sediments than the corresponding values in the HSSF; however, the aerobic and anoxic environments in the HSSF enhanced the removal of Cr with the co-precipitation of iron and manganese oxides, and their hydroxides. Metal concentrations in plant tissues were not significantly influenced by the concentrations in sediments, while roots contained statistically higher metal concentrations than stems and leaves. The sediments stored 94.01, 86.31, 95.85, and 89.51% of the total Cu, Pb, Cr, and Zn retained in the hybrid CW system, respectively, while only small fractions (<10%) were accumulated in the harvestable macrophyte tissues. It is important to clean not only the accessible sediments in free water surface tank and ponds but also the embedded sediments in vegetated beds for the sustainable removal of heavy metals.