Flood irrigation in the winter has been widely applied in northwest China for several years, but little attention has been paid to the flood irrigation program to date. In order to seek a reasonable irrigation quota, a flood irrigation experiment using two common quotas (1,800 and 1,200 m3 ha−1) was conducted in an area irrigated by saline water in the Nanjiang basin with shallow groundwater. Soil electrical conductivity in six treatments irrigated by saline water, with various salinity backgrounds, was investigated using Hydra and DDS-307 before and after flood irrigation. The results indicate that the quota of 12,00 m3 ha−1 was small enough to prevent soil salt from leaching out of the root zone. Although the quota of 1,800 m3 ha−1 may guarantee regular plant growth in the following year, it resulted in at least 267.2 g m−2 of salt entering the shallow groundwater. Therefore, flood irrigation had an important and profound effect on plants, soil environment, and shallow groundwater. The quota of flood irrigation in winter should be determined cautiously according to the hydraulic characteristics and salt background of the soil.