Based on electron acceptor abundance, Fe3+and SO2−4reduction by bacteria may play a dominant role in intrinsic bioremediation of some organic contaminants in the subsurface. Both Fe3+and SO2−4reduction processes involve mineral phases and may not be properly understood by evaluating only groundwater concentrations. Fe and S mineral analyses should be incorporated in natural attenuation studies; however, inherent problems with sample collection and analysis have discouraged such efforts. Methods are presented here for (1) sediment collection and anoxic preservation, (2) evaluation of biologically available Fe3+and biogenically produced Fe2+minerals, and (3) a simplified extended mineral sulfide analysis for ‐FeS and S°+FeS2. These techniques are demonstrated to evaluate Fe3+and SO2−4reduction at three sites where the soil or aquifer matrix had been contaminated with gasoline fuel, methane gas, or landfill leachate. It is expected that these techniques will permit Fe and S mineral analyses to become a routine part of natural attenuation assessments.