The influx of petroleum hydrocarbon into the aquifers due to piping leaks, an accidental spill of petroleum products, and leakage from underground fuel tanks at diesel and petrol pumps are some of the leading causes of aquifer pollution. This study presents a numerical model for subsurface investigation of benzene biodegradation in aquifers. Among the four BTEX (benzene, toluene, xylene, ethylbenzene) compounds, benzene is the most difficult to undergo degradation. This is because benzene has the highest C–H bond dissociation energy (473 kJ mol −1) among all the hydrocarbons. A fully implicit finite-difference approach is adopted here to analyse and solve the proposed numerical model, which is capable of obtaining the spatial variation in benzene concentrations. It is observed from the conducted research that biodegradation effectively limits the transport of benzene in aquifers. The investigation, in addition, can help in deducing the optimum rate at which electron acceptors are injected into the aquifer and the time required to reduce the concentration of benzene to desirable limits. The model also generates the scope of being used as a predicting tool for monitoring the efficacy of different biodegradation enhancement strategies in aquifers.