Technologically-mediated remediation of contaminated sites requires a detailed understanding of the biogeochemical processes that occur within the remediation treatment system. In the Lot 86 Superfund site, Raleigh, NC, dissolved manganese from influent groundwater is being microbially oxidized and precipitated, resulting in a dense Mn-oxide sludge that is obstructing the pump-and-treat remediation system. In this study, our objective was to evaluate the chemical composition and microbial community diversity within the Mn-bearing sludge. Sludge and water were collected from all points in the treatment system, and samples were analyzed using a comprehensive approach to better understand the evolution of system chemistry, mineralogy, and biology. Traditional (Sanger method) and high through-put (pyrosequencing) DNA sequencing techniques were carried out using 16S rRNA gene assays and nuclear ribosomal internal transcribed spacer (ITS) region assays to characterize the sludge and groundwater microbial isolates and community.  X-ray absorption spectroscopy, X-ray diffraction, and scanning electron microscopy with energy dispersive spectroscopy were utilized to characterize the mineralogy and morphology of sludge solids. Initial results reveal a variety of Mn-oxidizing microorganisms cultured from the treatment system, with most isolates being fungi and substantially fewer being bacteria. System mineralogy, dominated by layer-type Mn(IV) oxides, contains significant concentrations of Zn, Co, and Ba which are incorporated into specific binding sites on mineral surfaces. The sorption of metals to Mn oxides may remove metals from the aqueous phase during treatment. However, these metals could also be remobilized by reductive dissolution of Mn oxides, a process that may facilitate the breakdown of organic molecules in the influent stream. Accordingly, microorganisms play important roles in the treatment system, and may be of use for the design of novel biological remediation strategies.