The mechanism of surface water remediation in a natural wetland that is receiving heavy metal-rich acidic mine drainage was investigated. Selective sequential extraction was useful to derive the mechanisms of heavy metal removal in the wetland. In the upstream portion of the wetland, dissolved Fe was removed mainly as oxide-bounded mineral phases, such as hydroxides. These are important for the subsequent removal of other heavy metals. Other ion-exchangeable and carbonate-bounded heavy metals are also observed in the upstream, associated with Fe oxides. Organic matter and Fe–Mn oxides in the upstream remove Cu and Zn ions from the drainage, respectively. In the middle of portion of the wetland the removal of heavy metal ions in relatively low concentrations occurs by the emergent vegetation. Greater clay abundance and higher microbial activity of sulfate reducing bacteria in the downstream parts achieved low-level removal of metals. Multi-cell wetlands are recommended for the treatment of acidic metal bearing surface water drainage, if sufficient land area and expenses are available to construct.