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The assessment and control of losses of nitrogen (N) and phosphorus (P) from paddy fields is critical to improve the quality of water and atmosphere on earth. A field experiment was conducted to investigate the effect of three N managements (local common N fertilization practice, urea mixed with controlled-release N fertilizer, and optimized and reduced N fertilizer, designated CN, U + CRF and ON, respectively) on N and P losses through runoff and leaching from a paddy field, and yield of rice under shallow-irrigation and deep-sluice (SIDS) and continuous flooding irrigation (FI) in the Jianhan Plain of China in 2016. The results showed that, compared with FI, SIDS significantly reduced the frequency of irrigation and amount of irrigation water, resulting in an increase of 16.2% in rainfall use efficiency, and therefore, a reduction in the amount of surface runoff and water that had leached. This was responsible for the decreased total N (TN) and total P (TP) losses through runoff leaching under SIDS. The U + CRF and ON treatments resulted in a significant reduction in losses of TN through runoff and leaching and the loss of TP through leaching compared to CN. SIDS resulted in comparable or greater soil TN and TP contents in the 0–40 cm soil depths after rice harvest; N and P accumulation at the jointing, filling and maturity stages; and yield of grain compared to FI. Moreover, the U + CRF and ON improved or maintained accumulation of N and P and yield of rice compared to CN. Compared with FI coupled with CN, SIDS coupled with the U + CRF or ON treatments significantly reduced losses of N and P from paddy fields and enhanced or maintained the accumulation of N and P and yield of rice grains. In conclusion, SIDS coupled with the new N management could be an effective approach to reduce losses of N and P from paddy fields and would be a positive improvement for high yield of middle-season rice grains in the Jianhan Plain of central China and other regions with similar environments.

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