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Subsurface flow wetlands are one of the natural treatment methods used for municipal and industrial wastewater treatment that are economical in terms of energy consumption and cost-effectiveness. Much research has been conducted on wetland operation with continuous flow but not enough information is available on batch flow. This study investigates wetland efficiency in batch flow. For the purposes of this research, two pretreatment units of the anaerobic pond type with digestion pits and two subsurface flow wetlands with a 2-day detention time were built on the pilot scale. The cells were charged with sand of 5 mm effective size, uniformity coefficient of 1.5, and a porosity of 35%. One wetland cell and one pretreatment unit were used as control. The municipal wastewater selected to be monitored for the one-year study period had a flow rate of 26 m3/day and average BOD5 of 250mg/l, TSS of 320mg/l, TKN of 35mg/l, TP of 12mg/l and TC of 2×108 MPN/100ml from Sabzevar Wastewater Treatment Plant. The average removal efficiencies of BOD5,TSS,TKN,TP, and TC in the continuous flow for the combined control pretreatment and wetland cell were 77.2%, 92%, 91%, 89%, 96.5% while the same values for the batch flow for the combined experimental pretreatment and wetland cell were 92%, 97%, 97.5%, 97%, and 99.75%, respectively. The removal efficiency in the subsurface flow wetlands in the batch flow was higher than that of the continuous flow. Thus, for wastewaters with a high pollution level, the batch flow can be used in cell operation in cases where there is not enough land for spreading the wetland cell.