The conventional passive treatments for remediation of acid mine drainage using calcite are not totally efficient in the removal of certain heavy metal ions. Although pH increases to 6–7 and promotes the precipitation of trivalent and some divalent metals as hydroxides and carbonates, the remaining concentrations of some divalent metals ions do not fulfill the environmental regulations. In this study, Apatite II™, a biogenic hydroxyapatite, is used as an alternative reactive material to remove Zn(II), Pb(II), Mn(II) and Fe(II). Apatite II™ reacted with acid water releasing phosphate and increasing pH up to 6.5–7, inducing metals to precipitate mainly as metal–phosphates: zinc precipitated as hopeite, Zn3(PO4)2·4H2O, lead as pyromorfite, Pb5(PO4)3OH, manganese as metaswitzerite, Mn3(PO4)2·4H2O and iron as vivianite, Fe3(PO4)2·8H2O. Thus, metal concentrations from 30 to 75mgL−1 in the inflowing water were depleted to values below 0.10mgL−1. Apatite II™ dissolution is sufficiently fast to treat flows as high as 50m/a. For reactive grain size of 0.5–3mm, the treatment system ends due to coating of the grains by precipitates, especially when iron and manganese are present in the solution.