Bioremediation methods that precipitate contaminants in situ as solid (mineral) phases can provide cost-effective options for removing dissolved metals in contaminated groundwater. The current field-scale experiments demonstrate that indigenous bacteria can be stimulated to remove metals by injection of electron-donating substrates and nutrients into a contaminated aquifer. Groundwater at the investigation site is aerobic and contains high levels of lead, cadmium, zinc, copper, and sulfuric acid (pH = 3.1) derived from a car-battery recycling plant. During the experiments, lead, cadmium, zinc, and copper were almost completely removed by precipitation of solid sulfide phases, as pH increased from 3 to ∼5 and Eh dropped from +400 mV to −150 mV. X-ray and transmission electron microscopy (TEM) analyses of filtered material from the treated groundwater indicated the presence of newly formed nanocrystalline metal sulfides. Genetic sequencing indicated that the principal species of sulfate-reducing bacteria involved in the bioremediation process was Desulfosporosinus orientis. Geochemical modeling shows that oxidation of added substrates and subsequent bacterial sulfate reduction produced desired geochemical conditions (i.e., decreasing Eh and increasing pH) for the precipitation and sorption of metal sulfides. Geophysical survey results suggest that bioremediation lowers electrical conductance of groundwater and possibly increases the magnetic susceptibility of porous media. This study demonstrates that integrated geochemical, geophysical, and microbiological analyses, combined with theoretical modeling, can successfully track and predict the progress of subsurface bioremediation.