Manganese-oxidizing microorganisms are distributed in a wide range of environments. Amorphous biogenic manganese oxides play a significant role in the control of trace phase distribution in aquatic system. Some of them, which are tolerant to extremely high concentrations of Mn and have optimum pH less than 7, can be practically applied to treatment high Mn water, such as Mn-rich mine drainage. Additionally, the biogenic Mn deposits are poorly crystalline and significantly porous, providing highly efficient reaction fields in the environments, which are approached for decomposition and molecular size reduction of organic compounds like humic substances, oxidants, adsorbents of toxic metals, and so on.