Hurricane Isabel made landfall at the Outer Banks of North Carolina and moved past Chesapeake Bay on 18 –19 September 2003. The baroclinic response of this partially-mixed estuary to the passage of Isabel is investigated using the output from a regional atmosphere-ocean model. The hurricane-forced winds caused gradual deepening of the surface mixed layer, followed by rapid destratification in the water-column. The mixed-layer deepening appears to be driven by velocity shear and can be interpreted by a gradient Richardson number. Although strong winds caused complete mixing locally, a large longitudinal salinity gradient of about 10-4 psu m-1 persisted between the estuary's head and mouth. After passage of the storm, the horizontal baroclinic pressure gradient drove restratification and a two-layer circulation in the estuary. The averaged buoyancy frequency increased linearly with time during an initial stage, and reached about 0.03 s-1 one day after the destratification. The model results are in good agreement with the theoretical prediction based on gravitational adjustment. Subsequently, turbulent diffusion works against the longitudinal advection to produce quasi-steady salinity distribution.