Abstract: The influences of chlorination schemes on emitter clogging and system performance of drip irrigation systems applying secondary effluent and groundwater were investigated to determine optimum chlorination practices. In the experiments, six types of emitters with or without a pressure-compensating device and having a nominal discharge rate ranging from 1.0 to 2.6 L/h were used and three intermittent injections that maintained the residual chlorine concentration of 2.5, 5.0 and 10.0 mg/L at the end of the systems with an interval varying from one to four weeks were evaluated. The total duration of irrigation was 84 days, with a daily application of 12 hours. The results showed that all the chlorination schemes tested could effectively reduce the clogging in drip emitters applying sewage effluent, especially for the emitters with a nominal discharge rate of less than 1.38 L/h. A high system performance of statistical uniformity coefficient of greater than 90% could be obtained through intermittent chlorination. Although 99.9% of the total bacteria in the sewage effluent could be eliminated by the tested residual chlorine concentration of 2.5, 5.0, and 10.0 mg/L, the injection intervals of one week or two weeks were found to be more effective than the intervals of four weeks in reducing clogging due to biological growth. To maintain a high system performance, a chlorination scheme with low-concentration injection at high frequency is recommended.