Free-surface vortex formation is one of the undesirable hydraulic phenomena that may occur at intakes during the dewatering reservoir. This research is meant to investigate the effect of waves on formed vortices in vertical intakes numerically by applying STAR-CCM + software. The simulation was conducted to model the free surface and turbulence by volume of fluid and large eddy simulation methods, respectively. Sensitivity analysis was undertaken on different mesh sizes to select appropriate mesh dimensions. Then, verification was performed by Sun and Liu (J Hydraul Res 53:787-796, 2015) experimental data. Results showed that waves reduce or eliminate hydraulic parameters of the formed vortices such as vortex strength, tangential, radial, and axial velocity components. The reduction appeared by average values of 32%, 30%, 22%, and 25% in vortex strength, tangential, radial, and axial velocity components, respectively. Waves also led to decrement in the length and diameter of air-core of vortices about 45% for the former and more than 50% for the latter. In addition, it was concluded that the smaller the waves, the greater their effects would appear on the elimination of the vortex phenomenon. Finally, a relationship between the wave properties, as a hydraulic approach to anti-vortex, and vortex parameters was developed. Keywords Vertical intake • Surface wave • Free-surface vortex • Numerical simulation • STAR-CCM+ List of symbols P Pressure (kgm −1 s −2) u Velocity (ms −1) f i External force (kgms −2) g Gravity force (ms −2) V e Tangential velocity (ms −1) V r Radial velocity (ms −1) V z Axial velocity (ms −1) r Vortex radius (ms −1) Z Height from free surface (m) k T Turbulence kinematic energy σ Coefficient of surface tension Density (kgm −3) Dynamic viscosity (kgm −1 s −1) Reynolds-stress tensor (kgm −1 s −2) Kinematic viscosity (m 2 s −1) Eddy viscosity (m 2 s −1) e Effective viscosity (m 2 s −1) Γ Circulation (m 2 /s) ⃗ Angular velocity (rads −1) 2 r m V Γ in max Dimensionless parameter of tangential velocity (−Vrrm) e max Dimensionless parameter of radial velocity (V z r 2 m e z) max Dimensionless parameter of axial velocity