In this study, the efficiency of the permeable reactive barrier (PRB) in a column reactor using zero-valent iron (ZVI) particles and sand mixture in the removal of methyl tert-butyl ether (MTBE) from aquatic phases was investigated. The main operating parameters influence reactor performance such as pH, reaction time, pollutant content, catalyst load, hydraulic loading rate, and the reaction rate constant was evaluated. The results showed that the efficiency of process decreased with increasing pH, inflow, and pollutant concentration. In this case, the optimal conditions were obtained at pH=7, flow rate=0.23 m3/m2.d and C0=1 mg/L, which achieved a remarkable removal efficiency up to 90.32%. The being of high nitrate and hardness concentrations as intervening factors were led to reduce process efficiency to less than 44.61% and 51.4%, respectively. Lack of interfering factors had a considerable effect on the reaction rate of MTBE reduction that is approximately 2.65 and 4.11 times higher than in the presence of calcium hardness and nitrate, respectively. The PRB can be operated to remediate groundwater containing hydrocarbons based on filling media and hydraulic conditions.