An economic Cu-Zn volcanogenic massive sulphide (VMS) deposit was modeled in flow-through columns to examine the microbial controls on ore weathering and soil anomaly development. The presence of microorganisms, especially S- and Fe-oxidizing bacteria, increased the rate of weathering and metal release from ore. To examine the development of soil metal anomalies overlying the VMS deposit, flow-through experiments modeling the full overburden profile were completed. Selective extractions on the soil demonstrated that enhanced metal anomalies in the biotic column were developing in the reactive Fe- and Mn- oxide phases. These experimental results are linked to in situ biogeochemical processes through the use of Fe-oxidizing bacteria isolated from the deep subsurface of Triple 7 Cu-Zn VMS mine in Flin Flon, Manitoba, Canada, in direct proximity to where the ore material was collected. These results demonstrate that the rates of metal mobility in the subsurface and soil metal anomaly development at the surface are increased by the presence and activity of microorganisms when compared to control experiments.