Resource-conserving irrigation and fertilizer management practices have been developed for rice systems which may help address water quality concerns by reducing N and P losses via surface runoff. Field experiments under three treatments, i.e., farmers' conventional practice (FCP), alternate wetting and drying (AWD), and AWD integrated with site-specific nutrient management (AWD + SSNM) were carried out during two rice seasons at two sites in the southwest Yangtze River delta region. Across site years, results indicated that under AWD irrigation (i.e., AWD and AWD + SSNM), water inputs were reduced by 13.427.5 % and surface runoff was reduced by 30.236.7 % compared to FCP. When AWD was implemented alone, total N and P loss masses via surface runoff were reduced by 23.330.4 % and 26.931.7 %, respectively, compared to FCP. However, nutrient concentrations of surface runoff did not decrease under AWD alone. Under AWD + SSNM, total N and P loss masses via surface runoff were reduced to a greater extent than AWD alone (39.447.6 % and 46.148.3 % compared to FCP, respectively), while fertilizer inputs and N surpluses significantly decreased and rice grain yields increased relative to FCP. Therefore, by more closely matching nutrient supply with crop demand and reducing both surface runoff and nutrient concentrations of surface runoff, our results demonstrate that integration of AWD and SSNM practices can mitigate N and P losses via surface runoff from rice fields while maintaining high yields.