This study aimed to examine lab-scale constructed wetlands (CWs) for removing heavy metals from acid mine drainage (AMD). Two horizontal-subsurface-flow CWs filled with clamshells were prepared in parallel. One was planted with common reeds, while the other remained unplanted. Synthetic AMD containing 67.3 mg/L of Mn, 10.6 mg/L of Zn, and other minerals, with a pH of 5.3, was continuously fed to the CWs under hydraulic retention times (HRTs) of 12, 24, and 48h. Throughout the experimental period, clamshells with high CaCO3 contents exhibited great neutralization potential for AMD, with the effluent pH reaching 7.4–8.4. All clamshell-based CWs demonstrated high efficacy in removing Mn (83.6–92.3%), Zn (99.4–100%), and Cd, Cu, Fe, and Pb (97.8–100%) from AMD across all HRTs. However, slight Mn re-elution was noted at 48h. Higher removal efficiency was observed in the planted CWs, with all heavy metals meeting the effluent standards. Oxygen and organic matter exuded from the roots of common reeds can promote the growth of Mn-oxidizing microbes, leading to the precipitation of Mn oxides. The Mn and Zn concentrations correlated negatively with pH values, implying that Zn was removed as Zn hydroxide and adsorbed onto Mn oxide. The findings highlighted the potential of clamshells, an aquaculture byproduct, as a filter medium in CWs for AMD treatment. This study offers an ecological approach to reducing the environmental burden of seashell waste while lowering the cost of wastewater treatment.