Due to water limited, use of wastewater for agriculture is necessary. Drip irrigation system reduces the concerns associated with risk of sanitary and environmental contamination during use of wastewater because of water distribution near the plants or below the soil surface. But wastewater application aggravated emitter clogging. Chlorination, acidification and periodical lateral flushing are suggested techniques to prevent of emitter clogging. The aim of this study was to determine the effect of periodical lateral flushing and the combined use of acid and chlorine on prevent of emitter clogging in terms of wastewater application. The experimental treatments included nine main treatments, the interaction of the three chlorine concentrations, 10, 15 and 20 mg/L and three levels of pH, 6, 6.5 and 7 and two secondary treatments of wastewater application with and without periodical lateral flushing. The effect of these treatments on the performance of two emitter types, on-line and in-line pressure regulator emitter Netafim PCJ (4 L/hr) and UniRam (3.5 L/hr) were examined. To determine the effect of treatments in the performance of drip irrigation system, the discharge rate of eight specified emitters on each lateral was measured after three times irrigation (72 hours irrigation) and emission uniformity (EU), absolute emission uniformity (EUa), mean discharge rate (Dra), Christiansen’s uniformity coefficient (UC) and statistically uniformity coefficient (Us) of emitter discharge were evaluated. The results showed that relative performance for both of used emitters in the treatment of chlorination at a concentration of 10 mg/L, was better. But the performance of emitters rather than pH level, was different, so that the performance of PCJ emitter at pH of 6 and the performance of UniRam emitter at pH of 7, was better. The results also showed that in the condition of wastewater application, the performance of UniRam emitter was better than PCJ emitter.Furthermore the performance of PCJ and UniRam emitters in the terms of evaluated parameters, for all of studied treatment during the irrigation period was good. To determine the effects of chlorination on water and wastewater characteristics, the concentration of free residual chlorine, pH, electrical conductivity and concentrations of dissolved solids in the water and wastewater, following the injection of different chlorine concentrations were investigated. The results showed that the concentration of free residual chlorine changes by changing the concentration of added chlorine in the water and wastewater samples. However, changes in the concentration of free residual chlorine in wastewater samples with different levels of pH, with increasing concentrations of chlorine, were not clear trend. Although with increasing the concentrations of added chlorine to the water, free residual chlorine concentration was increased. To achieve the concentration of free residual chlorine to more than 1 mg/L, 1, 150 and 200 mg/L chlorine was used at water, wastewater samples at pH levels of 6and 6.5 and wastewater at pH of 7, respectively. By reduction of wastewater pH from 7 to 6-6.5, the amount of added chlorine to achieve free residual chlorine concentration at 1 mg/L, was decreased 25 percent. Although use of liquid sodium hypochlorite for chlorination of drip irrigation systems reduces the risk of biological clogging but increased concentrations of dissolved solids, salinity and pH of irrigation water that increases the risk of chemical clogging of emitters. Keyword : acidification, chlorination, drip irrigation system, emitter clogging, flushing, wastewater