Abstract: This article studied the effects of different tillage conditions, irrigation methods, and organic fertilizer substitution during the base fertilizer period on the organic carbon and nitrogen phosphorus concentrations, potential emissions, and rice yield in rice field surface water through pot experiments. The results showed that: (1) Compared with conventional irrigation, shallow water irrigation showed varying degrees of reduction in the average emission of various indicators under rotary tillage, including a 43.43% decrease in chemical oxygen demand (COD), a 43.19% decrease in dissolved organic carbon (DOC), a 46.52% decrease in total nitrogen (TN), and a 60.34% decrease in total phosphorus (TP). Under plow tillage, the COD, DOC, TN, and TP in the surface water of paddy fields decreased by 22.73%, 41.58%, 31.58%, and 31.25%, respectively. (2) Compared with rotary tillage, plow tillage reduced the average emission of COD, DOC, and TP in surface water of paddy fields by 16.02%, 15.67%, and 23.71%, respectively, during conventional irrigation. The average emission of COD, DOC, and TP in surface water of paddy fields decreased by 43.42%, 16.81%, and 13.93%, respectively, during shallow water irrigation. (3) There was no significant difference (P>0.05) in the average possible emission volume (APEV) of COD, DOC, and TP from surface water using organic fertilizer instead of nitrogen fertilizer as base fertilizer under shallow water irrigation. Compared with conventional irrigation, shallow water irrigation reduced rice yield by 20.63% and 6.88% under rotary tillage and plow tillage, respectively. In summary, the carbon, nitrogen, and phosphorus emission risks of shallow water irrigation field surface water are significantly lower than those of conventional irrigation. Plow tillage can effectively reduce the carbon, nitrogen, and phosphorus emission risks of field surface water. From the perspective of rice field surface water control and yield, shallow water irrigation and plow tillage can effectively reduce the risk of field surface water occurrence while ensuring rice yield. The research results can provide technical support for optimizing the application of rice field inputs and managing field water and nutrients.