The effect of the flow rate and water level on free surface vortices in a suction sump was studied by using numerical simulation. Free surface flow in an intake channel was solved by using finite volume method for RANS equations with k-ω SST turbulence model. A VOF multiphase model and the open channel model were used to solve the multiphase flow in the sump. Minimum position of air-water interface, air-entrained vortex length, air volume fraction contours and iso-surfaces were used to identify visually the location and shape of the free surface as well as surface vortices. From the numerical investigation with varying flow rate and water level, it was found that when the water level decreased or the flow rate increased, more free surface vortices appeared. The predicted velocity distributions at the entrance of bell mouth and the location of the center core of air-entrained vortices on the free surface were in good agreement with experimental results.