Hurricane Isabel made landfall along the North Carolina coast on September 18, 2003 (UTC 17:00) and the storm surge exceeded 2.0 m in many areas of the Chesapeake Bay and in the York River estuary. River flooding occurred subsequently, and the peak river discharge reached 317 and 104 m 3 s −1 in the Pamunkey and Mattaponi rivers, respectively. The York River estuary experienced both storm surge and river flooding during the event and the estuary dynamics changed dramatically. This study investigates the hydrodynamics of the York River estuary in response to the storm surge and high river inflows. A three-dimensional model was used to investigate the changes of estuarine stratification, longitudinal circulation, salt flux mechanisms, and the recovery time required for the estuary to return to its naturally evolved condition without the storm. Results show that the salt flux was mainly caused by advection, which was induced by the barotropic gradient during the storm event. The net salt flux increased by a factor of 30 during the rise of the storm surge. However, the large amount of salt transported into the estuary was quickly transported out of the estuary as the barotropic gradient reversed during the descent of the storm surge. Subsequent high freshwater inflow influenced the estuarine circulation substantially. The estuary changed from a partially mixed estuary to a very stratified estuary for a prolonged period. The model results show that it will take about 4 months for the estuary to recover to its naturally evolved salinity distribution after the impacts of the storm surge and freshwater pulse.