Sediment is an important environmental factor for aquatic ecosystem and oyster productivities of Apalachicola Bay located in Florida, USA. Based on the data analysis in this study, surface wind speed is highly correlated to the turbidity of water column, which results from sediment resuspension and transport in the Apalachicola Bay. In this paper, an application of a 3D sediment transport model to predict the wind-induced sediment transport in Apalachicola Bay is described. The sediment model is coupled with a 3D hydrodynamic module in the Environmental Fluid Dynamics Code (EFDC) model that provides information on estuarine circulation and salinity transport under normal temperature conditions. The hydrodynamic model was calibrated with field observations of water levels and salinity. The sediment transport model solves the transport equation with sources and sinks terms to describe sediment deposition and resuspension. The coupled hydrodynamic and sediment transport models were used to investigate wind-induced total suspended sediments (TSS) resuspension and transport in the bay. For the period June 1-July 30, 2005 two storm events with strong winds gave model results of TSS concentrations that compared well with the field observations. Model simulations reasonably reproduce the sudden increase of sediment concentrations during the storm events. Maximum sediment concentrations in the bay during the two storm events were 10 times or more than those in the pre-storm conditions. Spatial sediment transport from model simulations indicate active sediment resuspension and transport near areas of highly productive oyster beds. The model predictions of TSS and salinity can be used as inputs to an oyster dynamic model (Wang, H., Huang, W., Harwell, M., Edmiston, L., Johnson, E., Hsieh, P., Milla, K., Christensen, J., Stewart, J., Liu, X., 2008. Modeling eastern oyster population dynamics in response to changing environment in Apalachicola Bay, Florida. Journal of Ecological Modeling 211, 77-89) to support the ecological study of oyster growth and mortality in the aquatic ecosystem of Apalachicola Bay.