Unreasonable exploitation of groundwater resources in the Kongque River region has led to a decline in the groundwater table, groundwater salinization, and other geo-environmental problems. Therefore, this study supplements the studies on soil water and salt transport in the Kongque River region, and provides a new method for the prevention of groundwater salinization in arid and semiarid regions. In this study, soil column experiments were carried out to investigate the influence of lithological structures of the unsaturated zone, water quality, and methods of irrigation on soil water and salt transport. Based on the data from the experiment, a one-dimensional model of soil water and salt transport was built to predict the impact of long-term irrigation on groundwater quality using Hydrus- 1D. The results showed that groundwater TDS increased in the predicted scenarios and that groundwater quality was greatly influenced by irrigation water with high TDS values. The influence of long-term irrigation on groundwater quality was smallest for drip irrigation, which can save water and should be promoted. The influence of irrigation on groundwater quality was largest for flood irrigation. If flood irrigation cannot be avoided, then it is recommended that water with a TDS below 2 g/L should be used.