Hurricane Sandy was a large and intense storm with high winds that caused total water levels from combined tides and storm surge to reach 4.0 m in the Atlantic Ocean and 2.5 m in Great South Bay (GSB), a back-barrier bay between Fire Island and Long Island, New York. In this study the impact of the hurricane winds and waves are examined in order to understand the flow of ocean water into the back-barrier bay and water level variations within the bay. To accomplish this goal, a high resolution hurricane wind field is used to drive the coupled Delft3D-SWAN hydrodynamic and wave models over a series of grids with the finest resolution in GSB. The processes that control water levels in the back-barrier bay are investigated by comparing the results of four cases that include: (i) tides only; (ii) tides, winds and waves with no overwash over Fire Island allowed; (iii) tides, winds, waves and limited overwash at the east end of the island; (iv) tides, winds, waves and extensive overwash along the island. The results indicate that strong local wind-driven storm surge along the bay axis had the largest influence on the total water level fluctuations during the hurricane. However, the simulations allowing for overwash have higher correlation with water level observations in GSB and suggest that island overwash provided a significant contribution of ocean water to eastern GSB during the storm. The computations indicate that overwash of 7500–10,000 m³s⁻¹ was approximately the same as the inflow from the ocean through the major existing inlet. Overall, the model results indicate the complex variability in total water levels driven by tides, ocean storm surge, surge from local winds, and overwash that had a significant impact on the circulation in Great South Bay during Hurricane Sandy.