Manganese oxides produced by microorganisms are abundant environmental nanoparticles whose high retention capacity for toxic trace metals, especially lead, is well established. Until very recently, our knowledge of the molecular-scale structure and reactivity of these biogenic Mn4+ oxide minerals was inferred from studies of synthetic analogues prepared in the laboratory. However, biogenic Mn oxides and their reactions with trace metals now can be investigated directly using X-ray absorption spectroscopy, thus bringing new insights into the molecular mechanisms behind the very high scavenging efficiency of these minerals. This new knowledge has important implications for the remediation of trace metal contamination.