The salt marshes of Jamaica Bay serve as a recreational outlet for New York City residents, mitigate wave impacts during coastal storms, and provide habitat for critical wildlife species. Hurricanes have been recognized as one of the critical drivers of coastal wetland morphology due to their effects on hydrodynamics and sediment transport, deposition, and erosion processes. In this study, the Delft3D modeling suite was utilized to examine the effects of Hurricane Sandy (2012) on salt marsh morphology in Jamaica Bay. Observed marsh elevation change and accretion from rod Surface Elevation Tables and feldspar Marker Horizons (SET-MH) and hydrodynamic measurements during Hurricane Sandy were used to calibrate and validate the wind-waves-surge-sediment transport-morphology coupled model. The model results agreed well with in situ field measurements. The validated model was then used to detect salt marsh morphological change due to Sandy across Jamaica Bay. Model results indicate that the island-wide morphological changes in the bay's salt marshes due to Sandy were in the range of −30 mm (erosion) to +15 mm (deposition), and spatially complex and heterogeneous. The storm generated paired deposition and erosion patches at local scales. Salt marshes inside the west section of the bay showed erosion overall while marshes inside the east section showed deposition from Sandy. The net sediment amount that Sandy brought into the bay is only about 1% of the total amount of reworked sediment within the bay during the storm. Numerical experiments show that waves and vegetation played a critical role in sediment transport and associated wetland morphological change in Jamaica Bay. Furthermore, without the protection of vegetation, the marsh islands of Jamaica Bay would experience both more erosion and less accretion in coastal storms.