Currents in coastal zones under multiple mechanisms in terms of tides, waves, wind, and high roughness are difficult to model; bed shear stresses under wave–current flows are particularly challenging yet not being well studied. Few studies reported the modeling and validation of the bed shear stress in reef environments. In this paper, we present the first direct assessment of numerical modeling on depth-averaged currents and bed shear stresses over an algal reef using a coupled wave–current model (Delft-3D). The modeled results were validated and compared to the field observed data. The model considers hydrodynamic forcing in terms of tides, waves, wind stresses, and bed friction. Results show that the model generally reproduces the depth-averaged currents and bed shear stresses when considering all the mechanisms. Two numerical cases with and without wind forcing were tested to examine the effects of the winds. We found that the tide is mostly the primary factor driving the current, even in shallow waters within a depth of 3 m; however, the currents are also significantly affected by wind speeds and wind directions during high-wind events. When the wind direction is in the same direction as the tidal current, the current speed increases, suggesting the importance of the wind stress on the coastal currents. In addition, two models were chosen to study the nonlinear enhancement of bed shear stress by waves. We found a significant difference between the two models in predicting the bed shear stresses compared to the observed data. Nonlinear contribution from wave enhances the magnitude of bed shear stresses, which reduces the model error. The results highlight the nonlinear interaction between waves and currents is meaningful in predicting the bed shear stresses during high-wave-orbital motions; improvement of the present wave-current nonlinear interaction model for predicting the bed shear stresses may be needed.