In many natural and contaminated aquifers, geochemical processes result in the production or consumption of dissolved gases. In cases where methanogenesis or denitrification occurs, the production of gases may result in the formation and growth of gas bubbles below the water table. Near the water table, entrapment of atmospheric gases during water table rise may provide a significant source of O₂ to waters otherwise depleted in O₂. Furthermore, the presence of bubbles will affect the hydraulic conductivity of an aquifer, resulting in changes to the groundwater flow regime. The interactions between physical transport, biogeochemical processes, and gas bubble formation, entrapment and release is complex and requires suitable analysis tools. The objective of the present work is the development of a numerical model capable of quantitatively assessing these processes. The multicomponent reactive transport code MIN3P has been enhanced to simulate bubble growth and contraction due to in-situ gas production or consumption, bubble entrapment due to water table rise and subsequent re-equilibration of the bubble with ambient groundwater, and permeability changes due to trapped gas phase saturation. The resulting formulation allows for the investigation of complex geochemical systems where microbially mediated redox reactions both produce and consume gases as well as affect solution chemistry, alkalinity, and pH. The enhanced model has been used to simulate processes in a petroleum hydrocarbon contaminated aquifer where methanogenesis is an important redox process. The simulations are constrained by data from a crude oil spill site near Bemidji, MN. Our results suggest that permeability reduction in the methanogenic zone due to in-situ formation of gas bubbles, and dissolution of entrapped atmospheric bubbles near the water table, both work to attenuate the dissolved gas plume emanating from the source zone. Furthermore, the simulations demonstrate that under the given conditions more than 50% of all produced CH₄ partitions to the gas phase or is aerobically oxidised near the water table, suggesting that these processes should be accounted for when assessing the rate and extent of methanogenic degradation of hydrocarbons.