A pond-ditch circulation system (PDCS) shows great promises for ecological restoration of rural contaminated water in southern China. In this study, the optimal flow speed, circulation interval, and their combination for the system were investigated for higher pollutant removal efficiency and lower costs in three separate experiments: I, II, and III, respectively. In each experiment, there are three PDCSs (S1, S2, and S3) with different water circulation speeds or circulation intervals, respectively. The results demonstrated that in experiment I, total nitrogen (TN) removal rates, species numbers, and diversity indexes of zooplankton in S1 with a flow speed of 3.6 L/h were significantly higher than those in S2 (7.2 L/h) and S3 (10.2 L/h), respectively. Similarly, in experiment II, S3 circulating every other 4 h had significantly higher TN reduction rates, species numbers, and diversity indexes than S1 and S2 circulating every other 1 and 2 h, respectively. In experiment III, water qualities in S1 (circulation of 3.6 L/h + interval of 4 h) were better than those in S2 (7.2 L/h + 4 h) and S3 (10.2 L/h + 6 h), respectively. Together, circulation at every other 4 h (3.6 L/h) is probably the optimal operating condition for the PDCS in remediating rural contaminated water.