Today, groundwater contamination has become a major environmental issue around the world. Petroleum products affect groundwater quality at many sites across the country. It mainly results from leaking or seeping of products from storage tanks or transferring pipes. These products are typically multicomponent organic mixtures composed of chemicals with varying degrees of water solubility. Many of the petroleum products are amenable to biological degradation in the aqueous phase by naturally occurring microorganisms in the subsurface. To create and maintain conditions that are conductive to microbial activity within the contaminated aqueous-phase is the main focus of this research. BTEX was selected as the petroleum contaminant to be used in a laboratory experiment. A two-dimensional sand tank was built and BTEX was injected into the sand at top of the unsaturated zone. In order to simulate the behaviour of the bacteria and to predict the long-term remediation program, RT3D model with double Monod algorithm was selected. The comparison of the observed data in laboratory experiment with simulated results showed that the calibrated model can simulate the BTEX movement and biodegradation, satisfactory. Using the calibrated model indicated that complete remediation would occur after three months with biodegradation and 27 months without biodegradation. This proved that how important is the biodegradation in long-term remediation projects. In addition, the proposed methodology in this research for isolating the bacteria and remediation was successful and can be proposed to be implemented in larger scale.