In recent decades, groundwater overexploitation has caused an important aquifer level decline in arid zones each year. In addition to this issue, large volumes of effluent are produced each year in metropolitan areas of these regions. In this situation, an aquifer storage and recovery system (ASR) using the reclaimed domestic wastewater can be a local solution to these two challenges. In this research, a post-treatment of reclaimed municipal wastewater has been investigated through unsaturated–saturated porous media. A large-scale, L-shaped experimental model was set up near the second-stage wastewater treatment plant (WWTP) in the west of greater Tehran. The water, soil, and treated wastewater of the experimental model were supplied from the aquifer, site, and WWTP, respectively. The 13 physicochemical parameters, temperature and fecal coliform were analyzed every 10 days in seven points for a period of four months (two active periods of 40 days with a 12-h on–off rate (wet cycles) and a rest period of 40 days (dry cycle) between the two wet cycles). The results showed that the effects of the saturated zone were twice as great as those of the unsaturated zone and two-thirds of the total treatment efficiency. Furthermore, a discontinuous wet–dry–wet cycle had a significant effect on effluent treatment efficiency and contaminants’ reduction. In conclusion, an aquifer storage and recovery system using treated wastewater through the unsaturated–saturated zones is a sustainable water resource that can be used for agriculture, environmental and non-potable water demands.