Alternate drought and flooding stress has become more prevalent during paddy growth stages as a result of climate change, especially in southern China. This study aims to assess the effect of alternate drought and flooding stress on water use, and nitrogen (N) and phosphorus (P) losses in paddy fields. Two controlled irrigation and drainage (CID) managements (namely drought at the beginning of growth stages followed by flooding (CID-1), and flooding at the beginning of growth stages followed by drought (CID-2) and one alternated wetting and drying (AWD) management were designed in specially designed experimental tanks with three replications in 2015 and 2016. Results showed that CID increased effective irrigation quantities and rainwater storage ability with a significant decrease in water use efficiency compared with AWD. For surface water, CID-1 significantly improved possible losses of nitrogen and phosphorus during the fertilizer application period over CID-2. For subsurface water, CID can significantly reduce the leaching losses of nitrate N and P compared with AWD. Meanwhile, CID-1 significantly increased the leaching losses of nitrate N at the former two growth stages compared to CID-2, yet no significant difference was found for ammonia N and P. Therefore, the application of controlled irrigation and drainage – especially for CID-1 – was an efficient method for obtaining high water quality and reducing eutrophication.