The ungauged Sugan Lake Basin represents a candidate area for development of a water transfer scheme to satisfy the water requirement of Dunhuang city in northwestern China. In this work, multisource data, including river runoff, groundwater levels and remote-sensing data, and field investigation records, were collected and analyzed. A three-dimensional groundwater flow model was constructed using FEFLOW software to predict the potential influence of the transfer project on the groundwater system. Results show that infiltration from the Great Harten River is the main driving factor of groundwater-level fluctuation and groundwater recharge. Scenario analysis under four water transfer conditions found that the drawdown of groundwater gradually decreases from east to west. If the water transfer scale reaches 1.2 × 10⁸ m³/a, after 100 years, the maximum drawdown of groundwater is noted at 68.02 m, and the flow rate of the Middle Spring reduces by 25.7%. In the western wetland, the area over which the groundwater level is lowered by more than 4 m is 10.21 km², and natural succession may occur or vegetation cover may decline. The results of this study will aid in water resource planning based on a rational amount of water transfer, and provide further protection of the wetland ecology.