[Purposes] This paper aims to clarify the adverse effects of prolonged dry seasons and low water levels in northern Dongting Lake on the water supply efficiency of the gate-pump system within the area after the operation of the Three Gorges Project and evaluate the recovery of water supply efficiency of the gate-pump system after the completion of the second phase of the Zoned Water Refill Project in northern Dongting Lake, so as to provide a reference for the decision-making of the rectification and construction plan of the gate-pump system and the optimization of the regional major water resources allocation project planning. [Methods] Based on the daily water level data of main hydrological/water level stations in the study area from 1988 to 2017, cluster analysis and trend testing were used to study the duration and variation of low water levels during the dry season before and after the operation of the Three Gorges Project. The differences in water source structure, water supply types, and water supply efficiency of the gate-pump system of each embankment before and after the completion of the second phase of the Zoned Water Refill Project were compared. [Findings] After the operation of the Three Gorges Project, the dry season of the study area is advanced and extended by 1.4-13.7 d, and the average water level during the dry season decreases by about 0.30-0.42 m. After the implementation of the second phase of the Zoned Water Refill Project, the water supply of different water sources will be more balanced. The average water supply efficiency of the gate group increases by 2.8%, 2.1%, and 12.9% in normal, dry, and ultra-dry years, and the average water supply efficiency of the pump group decreases by 74.2%, 45.5%, and 47.3% respectively. [Conclusions] Since the operation of the Three Gorges project, the hydrological regime of the study area during the dry season has changed significantly. The implementation of the second phase of the Zoned Water Refill Project can alleviate the regional water shortage problem. It is suggested that the inefficient gate-pump system in the study area can be removed later, and the water storage project and cross-embankment water transfer project can be supplemented.