Abstract Salinity is an important factor for oyster and estuarine productivity in Apalachicola Bay. Observations of salinity at oyster reefs have indicated a high correlation between subtidal salinity variations and the surface winds along the bay axis in an approximately east–west direction. In this paper, we applied a calibrated hydrodynamic model to examine the surface wind effects on the volume fluxes in the tidal inlets and the subtidal salinity variations in the bay. Model simulations show that, due to the large size of inlets located at the east and west ends of this long estuary, surface winds have significant effects on the volume fluxes in the estuary inlets for the water exchanges between the estuary and ocean. In general, eastward winds cause the inflow from the inlets at the western end and the outflow from inlets at the eastern end of the bay. Winds at 15 mph speed in the east–west direction can induce a 2000 m 3 s −1 inflow of saline seawater into the bay from the inlets, a rate which is about 2·6 times that of the annual average freshwater inflow from the river. Due to the varied wind-induced volume fluxes in the inlets and the circulation in the bay, the time series of subtidal salinity at oyster reefs considerably increases during strong east–west wind conditions in comparison to salinity during windless conditions. In order to have a better understanding of the characteristics of the wind-induced subtidal circulation and salinity variations, the researchers also connected model simulations under constant east–west wind conditions. Results show that the volume fluxes are linearly proportional to the east–west wind stresses. Spatial distributions of daily average salinity and currents clearly show the significant effects of winds on the bay.