This study explores the scour phenomenon around a submerged square pile under the combined influence of waves and currents. To this end, a three-dimensional Computational Fluid Dynamics model was developed. The numerical model solves the Reynolds-averaged Navier-Stokes (RANS) equations with k-ω turbulence closure model. The Level-Set method is utilized to monitor free surface interface realistically within the computational model. The Exner formulation is used to compute the bed elevation variations. An extensive validation is conducted for square pile scour in steady current, wave only, and wave–current conditions. Subsequently, the validated numerical model is utilized to analyze the impact of the submergence ratio, wave-current parameter (U_cw), and Keulegan–Carpenter (KC) number on the normalized scour depth around the submerged square pile in combined wave-current flows. The numerical results show that an increase in submergence ratio leads to an increased normalized scour depth around submerged piles in wave-current flows. Furthermore, it was found that a larger U_cw results in a larger normalized scour depth around the submerged square pile. However, for larger KC values of 12 and 18, the effect of U_cw becomes negligible due to the suppression of lee-wake vortices by developed trailing vortices.