In February 2014, a persistent and strong northerly wind caused an extremely severe saltwater intrusion event in the Changjiang Estuary, which posed a threat to the safety of water intake from this source. Increasing river discharge from upstream reservoirs in the river basin is a method to combat severe saltwater intrusion. To simulate and analyze the effects of various river discharges on saltwater intrusion, we used the Unstructured quadrilateral grid, Finite-differencing, Estuarine and Coastal three-dimensional Ocean numerical Model (UnFECOM). By taking into account realistic river discharge and wind conditions, the model accurately reproduced the extremely severe saltwater intrusion process that occurred in February 2014. Our findings indicated that the net water flux (NWF) across the section at the upper reaches of the North Channel (NC) remained landward during the most critical period of saltwater intrusion from February 10 to 13, 2014, despite the increase in river discharge. However, the magnitude of NWF tended to decrease with increasing river discharge. The net water diversion ratio (WDR), NWF (Net Water Flux), and salt flux increased with the increase in river discharge. Under realistic river discharge conditions, WDR was –29% (the negative sign indicates that the NWF is landward), NWF was –2300 m ³/s, and the net salt flux (NSF) was –68 t/s, indicating that the NWF and NSF were landward due to the landward Ekman transport effect induced by the persistent severe northly wind. When the river discharge increased by 3000 m ³/s, WDR and NWF across the section were nearly zero, and NSF was –34 t/s. When the river discharge increased by 8000 m ³/s, WDR was 21.5% and NWF was seaward, at 3550 m³/s. NSF was –6 t/s and landward. At the water intake of Qingcaosha Reservoir, the longest continuous unsuitable water intake time decreased slightly when the river discharge increased by less than 4000 m ³/s. When the river discharge increased to 5000 m³/s, the longest continuous unsuitable water intake time decreased significantly to 10.5 days. It may be challenging to achieve the necessary value and duration of river discharge increase required for the actual operation of the Three Gorges Reservoir. To ensure the safety of water intake, implementing an early warning and forecasting system for saltwater intrusion and storing water into the reservoir at a high level before the intrusion occurs are recommended as effective methods.