The permeable reactive barrier (PRB) has been used as an in-situ remediation for the contaminated groundwater by heavy metals, organic compounds, and radioactive nuclide. Deep aquifer remediation tool (DART) has been developed for contamination treatment of deep underground environment. In this study, we proposed a method of deep aquifer treatment composed with pile type PRB and groundwater control, and investigated the effect of the design factors and the operation conditions on the effectiveness of PRB system using numerical modeling approach. Conceptual models were developed considering various configuration of reactive wells and extraction well for groundwater control. The groundwater flow was simulated using MODFLOW. Capture zone and residence time were analyzed using particle tracking (MODPATH) to evaluate the effectiveness of PRB system. Sensitivity analysis was carried out by considering the various hydrogeological conditions of the surrounding aquifers, the design factors, the PRB configuration (interval, depth) and the conditions of groundwater control (extraction and injection). Results have shown that pile type PRB can prevent spreading groundwater contamination successfully by use of appropriate configuration of reactive wells and groundwater control. For the case of using extraction well, the capture zone increased with increase in extraction rate, but the residence time decreased.