Metal contamination of soils is a widespread problem at many current and former industrial and military sites. Lead, arsenic, chromium, and cadmium are of particular concern because of their toxicity and potentially harmful effects on the environment. In situ immobilization is a desirable strategy for reducing metal bioavailability through precipitation or adsorption by adding chemical amendments to contaminated soils. Speciation is the key factor in controlling mobility and bioavailability of metals in soils, and information of the mineralogy and geochemistry of contaminant metals can provide important information for risk assessment and remediation strategies. We sampled a Histosol in a peat bog that receives runoff and seepage water from the site of a former lead smelter. We used the synchrotron x-ray microprobe on beamline X26A at the National Synchrotron Light Source at Brookhaven National Laboratory to obtain micro x-ray diffraction patterns (µ-XRD) and micro x-ray fluorescence patterns (µ-XRF) of each aggregate. Arsenic and chromium x-ray absorption near edge structure (XANES) spectra were then obtained for aggregates with significantly high level of arsenic or chromium. Results show a clear pattern of metal speciation changes with depths. The oxidized yellow surface layer was dominant by goethite and a poorly crystalline phase that is probably schwertmannite. Pb and As were highly associated with these Fe oxyhydroxides. Fe(II)-containing minerals, such magnetite siderite and possibly wustite were identified in subsurface layers. A number of sulfide minerals have been identified in the most reduced horizons at depths > 30 cm. They include realgar, greigite, galena, and sphalerite, alacranite, and others. Most of these minerals occur as almost pure phases in the submillimeter aggregates and appear to be secondary phases that have precipitated from solution. Mineralogical and chemical heterogeneity and the presence of phases stable under different redox conditions make this a challenging soil for in situ remediation.