Synchrotron radiation-induced micro-X-ray analysis were applied to characterize the newly formed phases that precipitate in a passive treatment system using magnesium oxide to remove high concentrations of zinc (ca. 440 mg/L) and other minor metals from neutral pretreated waters in the Iberian Pyrite Belt (SW Iberian Peninsula). Micro-X-ray fluorescence (μ-XRF) maps of polished samples were used to find spatial correlations among metals, pinpointing zones of interest where micro-X-ray diffraction (μ-XRD) data were exploited to identify the mineral phases responsible for metal retention. This coupled technique identified hydrozincite (Zn(5)(CO(3))(2)(OH)(6)) and minor loseyite ((Mn,Zn)(7)(CO(3))(2)(OH)(10)) as the mineral sinks for Zn and also other potentially toxic elements such as Co and Ni. Although hydrozincite retains traces of Mn, this metal is mainly retained by precipitation of loseyite. The precipitation of zinc hydroxy-carbonates and their ability to uptake other metals (Mn, Co, and Ni) is hence of potential interest not only for the treatment of contaminated waters but also for the generation of a solid waste that could be exploited as a new Zn economic resource.