Subsurface limestone beds (SLBs) are passive treatment systems for removing toxic metals from acid mine drainage (AMD). This study investigated metal precipitation mechanisms in an SLB at the Motokura Mine, Japan. Field surveys showed pH increasing to ~8, causing hydroxide/carbonate precipitation of Cu, Zn, and Pb. Mn and Cd removal occurred at lower pH (7–8) due to δ-MnO₂ formation by manganese-oxidizing bacteria, followed by Cd surface complexation with MnO₂. Biological agents enhanced metal removal, suggesting their utilization could improve SLB performance.