Estuarine process‐oriented modelling studies were undertaken to understand bottom boundary layer processes in Tampa Bay, Florida. A stationary shallow water wave model, SWAN, was applied to predict wind wave‐induced rms bottom orbital currents in Tampa Bay on a 70 × 100 curvilinear grid. Simulations were performed by using two idealized wind forcing (i.e. northeasterly winds of 10 and 20 m s−1) and high‐resolution bathymetry. Calculations of bed load and total load of fine sand were made by using the transport formulas of Van Rijn (J. Hydraulic Eng. 1984; 110:1431–1456) and Engelund–Hansen (A Monograph on Sediment Transport in Alluvial Streams. Copenhagen Technical Press: 1972), respectively. Simulations of wind wave induced currents reveal that they are important for fine sand transport along the shallow margins of the Tampa Bay. Modelled bottom orbital currents ranged from 0.05 to 0.39 m s−1. Total loads of fine sand ranged from 2.26×10−10 to 1.05×10−5kg m−1 s−1 for northeasterly winds of 10 m s−1 and from 2.46×10−5 to 3.21×10−5 kg m−1 s−1 for northeasterly winds of 20 m s−1. Wind wave‐induced bottom resuspension is an important process affecting water quality in Tampa Bay.