The valve shaft of Gezhouba dam ship lock is connected to the transmission gallery of the river area. During the flood season of 1993, the water level in the valve shaft increased abnormally, jeopardizing the safety of the lock’s equipment and facilities. To investigate the causes of the abnormal water level rise in the valve shaft of the Gezhouba ship lock, we examined the quantitative relationship between high-sediment-concentration flow and abnormal water levels. Using the Mike-3D numerical model, we simulated the vertical distribution of flow and sediment concentration under various discharge rates and sediment concentrations. We then calculated the relationship between the abnormal water levels in the valve shaft and sediment concentration. Based on these simulations, we explained the abnormal water level increases in the two valve shafts of the Gezhouba ship lock during 1993. Finally, we assessed the likelihood of future abnormal water level increases in the valve shafts. The modelling result reveals that the discharge and sediment concentration at approximately (30 000 m³/s, 2.85 kg/m³), (40 000 m³/s, 1.42 kg/m³), and (50 000 m³/s, 1.23 kg/m³), respectively, would lead to the abnormal water level increase exceeding 0.5 m. Following the construction of cascade reservoirs in the upstream and the implementation of China’s policy of returning farmland to forests, the probability of water level rise exceeding 0.5 m is now quite low. The findings offer valuable management insights for the safe operation of the Gezhouba ship lock.