Controlled irrigation and drainage (CID) has received considerable attention as a reliable management practice for improving water quality and water productivity in rice production. This study aimed to evaluate the effects of CID on water productivity, nitrogen, and phosphorus losses in paddy fields. Treatments include alternate wetting and drying (AWD; lower limit of irrigation to -200 mm and upper limit of ponding water depth after rainfall to 60 mm), CID-I (lower limit of irrigation to -200 mm and upper limit of ponding water depth after rainfall to 200 mm), and CID-II (lower limit of irrigation to -500 mm and upper limit of ponding water depth after rainfall to 200 mm). Results showed that CID reduced irrigation water without a significant impact on grain yields and increased the irrigation water productivity by 14.6-51.5% compared with AWD. However, the percolation of CID may be increased, especially in a wetting year. The application of CID-II by combining yield with irrigation water productivity could be suitable and beneficial to rice crops. The average total nitrogen (TN) and total phosphorus (TP) concentrations of CID presented similar values or were significantly increased relative to AWD, indicating that the significant decreases in nutrient loads under CID were primarily due to reductions in surface runoff rather than changes in concentration. Ammonium nitrogen (NH₄⁺-N) concentrations were clearly increased after fertilizer application in percolation water. Compared with AWD, the NH₄⁺-N, TN, and TP leaching losses of CID-I were increased. The nitrogen and phosphorus leaching losses of CID-II were significantly increased relative to AWD and CID-I because of high nutrient concentrations and severe preferential flow. Therefore, CID potentially increased nitrogen and phosphorus loading to groundwater when the lower limit irrigation was used. The results indicate that the suitable application of CID can save fresh water, reduce nutrient losses, and guarantee rice production.