Various potentially toxic trace elements such as As, Cu, Pb and Zn have been remobilized by the weathering of a sulfide orebody that was only partially mined at Leona Heights, California. As a result, this body has both natural and anthropogenically modified weathering profiles only 500 m apart. The orebody is located in a heavily urbanized area in suburban Oakland, and directly affects water quality in at least one stream by producing acidic conditions and relatively high concentrations of dissolved elements (e.g., ~500 mg/L Cu, ~3700 mg/L Zn). Micrometric-scale mineralogical investigations were performed on the authigenic metal-bearing phases (less than 10 mm in size) using electron-probe micro-analysis (EPMA), micro-Raman, micro X-ray absorption spectroscopy (mXAS), scanning X-ray diffraction (mSXRD) and scanning X-ray fluorescence (mSXRF) mapping techniques. Those measurements were coupled with classical mineralogical laboratory techniques, X-ray diffraction (XRD) and scanning electron microscopy (SEM). Authigenic metal-bearing phases identified are mainly sulfates (jarosite, epsomite, schwertmannite), Fe (oxy-)hydroxides (goethite, hematite and poorly crystalline Fe products) and poorly crystalline Mn (hydr-)oxides. Sulfates and Fe (oxy-)hydroxides are the two main secondary products at both sites, whereas Mn (hydr-) oxides were only observed in the samples from the non-mining site. In these samples, the various trace elements show different affinities for Fe or Mn compounds. Lead is preferentially associated with Mn (hydr-)oxides and As with Fe (oxy-)hydroxides or sulfates. Copper association with Mn and Fe phases is questionable, and the results obtained rather indicate that Cu is present as individual Cu-rich grains (Cu hydroxides). Some ochreous precipitates were found at both sites and correspond to a mixture of schwertmannite, goethite and jarosite containing some potentially toxic trace elements such as Cu, Pb and Zn. According to the trace element distribution and relative abundance of the unweathered sulfides, this orebody still represents a significant reservoir of potential contaminants for the watershed, especially in the non-mining site, as a much greater proportion of sulfides is left to react and because of the lower porosity in this site.