The transport of gas phase carbon dioxide through unsaturated soils has the potential to significantly alter the soil biogeochemistry. Leakage of CO2 from deep reservoirs, either naturally occurring or anthropogenically emplaced, may displace oxygen in the soil gas and hence radically alter the redox conditions of a soil. Furthermore, the formation of carbonic acid in the aqueous phase will alter the pH of the soil system. A two-dimensional numerical model has been developed to explore the effects of gaseous CO2 leakage on the biogeochemistry of a variably saturated porous media. The model describes the sequential degradation of organic carbon by microorganisms using a series of terminal electron acceptors. Gas phase CO2 intrusion results in changes in redox conditions and pH of the soil water, both of which lead to alteration of the biogeochemistry of the soil. Alteration of the biogeochemical profile of a representative field site is explored with the numerical model.