Secondary Fe(III) oxyhydroxides play a key role in controlling the mobility and bioavailability of trace metals in acidic, sulfate-rich soils, such as mining and smelter sites. Schwertmannite, jarosite, goethite, and ferrihydrite are the most common mineral phases identified in such soils. A good understanding of the precipitation and transformation of these minerals in soils is very important for predicting the mobility and long-term stability of trace metals associated with them. In the present study, bulk powder X-ray diffraction (XRD), scanning electron microscopy (SEM), synchrotron based micro-X-ray diffraction (μ-XRD), and micro X-ray fluorescence (μ-SXRF) spectroscopy were used to investigate precipitates from the surface horizon of an organic soil (Histosol) at a site that once contained a lead smelter. Soil samples were collected from 0 to ~10 cm depth during both wet and dry seasons. Goethite and akaganeite were identified as the major mineral phases in this soil. Schwertmannite and jarosite were also occasionally identified, particularly in the soil samples from dry periods. The peaks in the akaganeite XRD pattern were significantly broadened and the relative intensities of some major peaks were distinctly different compared with the diffraction pattern of synthetic akaganeite, possibly due to the effects of pH and the incorporation of sulfate. The SEM and μ-XRD data support the hypothesis that the goethite in the precipitates is not the product of direct precipitation from solution but the transformation of previously precipitated schwertmannite or akaganeite.