Geophysical investigations documenting enhanced magnetic susceptibility (MS) within the water table fluctuation zone at hydrocarbon contaminated sites suggest that MS can be used as a proxy for investigating microbial mediated iron reduction during intrinsic bioremediation. Here, we investigated the microbial community composition over a 5-year period at a hydrocarbon-contaminated site that exhibited transient elevated MS responses. Our objective was to determine the key microbial populations in zones of elevated MS. We retrieved sediment cores from the petroleum-contaminated site near Bemidji, MN, United States, and performed MS measurements on these cores. We also characterized the microbial community composition by high-throughput 16S rRNA gene amplicon sequencing from samples collected along the complete core length. Our spatial and temporal analysis revealed that the microbial community composition was generally stable throughout the period of investigation. In addition, we observed distinct vertical redox zonations extending from the upper vadose zone into the saturated zone. These distinct redox zonations were concomitant with the dominant microbial metabolic processes as follows: (1) the upper vadose zone was dominated by aerobic microbial populations; (2) the lower vadose zone was dominated by methanotrophic populations, iron reducers and iron oxidizers; (3) the smear zone was dominated by iron reducers; and (4) the free product zone was dominated by syntrophic and methanogenic populations. Although the common notion is that high MS values are caused by high magnetite concentrations that can be biotically formed through the activities of iron-reducing bacteria, here we show that the highest magnetic susceptibilities were measured in the free-phase petroleum zone, where a methanogenic community was predominant. This field study may contribute to the emerging knowledge that methanogens can switch their metabolism from methanogenesis to iron reduction with associated magnetite precipitation in hydrocarbon contaminated sediments. Thus, geophysical methods such as MS may help to identify zones where iron cycling/reduction by methanogens is occurring.