The hydraulic performance of water intake system is strongly influenced by the geometry of the pump intake and the approaching flow conditions. Undesirable vortices and the suction of air will be induced if a poor design of the system is made. An open pump intake was referred so that both the free-surface and sub-surface vortices could be taken into account under the influence of the geometry and neighboring flows. Large eddy simulation (LES) was employed to simulate the flow and the associated vortices in the pump intake and the fluctuation of free surface was resolved by means of volume of fluid model (VOF). The verification and validation of the simulated results were systematically performed. On the one hand, the mesh size near the wall was checked with y+ and the LES index of quality (LES_IQ) was calculated which demonstrated the percentage of directly resolved turbulent kinetic energy in LES by using two sets of meshes with different grid quantities. On the other hand, the numerical results were compared with the well-known published experiments with respect to the transient flow feature and time-averaged vorticity profile, where the disparities were also analyzed. Compared with most Reynolds averaged Navier-Stokes (RANS) based simulations, LES showed a better prediction for all kinds of vortices on location, shape, size of vortex core, velocity, as well as the turbulence kinetic energy inside vortex core. Based on the numerical results, time-averaged behavior of three typical vortices showed better similarities with reality that there was always a core region surrounding the axis where the azimuthal velocity stopped increasing and decreased to zero as radius went to zero. Besides, iso-surface of λ2 was adopted to visualize the vortices at different times, showing the main vortex and spirally rounding vortical structures. Transient behaviors of free surface and submerged vortices were analyzed, and the effects of advection and stretching/tilting termed on the vorticity variation were discussed via vorticity transport equation.