We investigated the hydrodynamic and morphologic response of Barnegat Bay-Little Egg Harbor, New Jersey, USA to Hurricane Sandy. We implemented a three-dimensional, coupled ocean-wave-sediment transport model of the estuary and explored the role of offshore water levels, offshore waves, local winds and waves by systematically removing forcings from a series of simulations. Offshore water levels had the largest impact on water levels in the bay while waves and local wind forcing created substantial spatial variation along the longitudinal axis of the bay. The shape of the bay and its orientation relative to the storm track influenced the response to winds and restricted the maximum water levels in the northern bay and reduced the maximum volume of surge. Basin-average hydrodynamic residence time was reduced by 40%, though its typical spatial distribution remained during the storm. Wave and current-induced bed shear stress resuspended fine sediment resulting in net erosion from the shoals with ensuing net deposition over fringing low-lying land. The net sediment exchange between the bay and the ocean was several times smaller than the exchange at the peak of the storm resulting in negligible net change in the bay volume. Overall, our results suggest that water level responses are highly sensitive to the specific orientation of storm winds relative to the estuary, thereby limiting the utility of simple inundation models. The sediment transport patterns indicate that storms are an important mechanism for redistributing sediment from shoals to fringing wetlands, while net change to sediment budget can be negligible.