Just a guess that the Mn is ...

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Just a guess that the Mn is in solution as Mn2+ ions which implies that  conditions are reducing.  One way of removing the manganese might be to install an oxidizing substrate filter such as granular MnO2, followed by a water softener. These would need to be changed periodically as reducing conditions will eventually resolubilize the Mn. Aeration, followed by simple filtration (perhaps using chalk) might be enough.