Well-resolved detached eddy simulation (DES) and unsteady Reynold-averaged Navier–Stokes (URANS) simulations are conducted for a water pump-intake bay. Three cases are analysed: a high-submergence, low discharge case (Case 1), a low-submergence, low-discharge case (Case 2) and a low-submergence, high-discharge case (Case 3). The numerical model uses the volume of fluid (VOF) to account for the free surface deformations. In Case 1, for which the free surface deformations in the experiment were small, DES predictions are in better agreement with previous experimental measurements, compared to URANS predictions of the mean flow position, circulation, mean azimuthal velocity and vorticity distribution inside the cores of the main free-surface and submerged vortices forming inside the pump-intake bay. Decreasing the submergence depth in Case 2 results in an intensification of the coherence and unsteadiness of the main free surface vortex and in notable deformations of the free surface compared to Case 1. In Case 3, where the discharge is five times larger compared to Case 2, DES predicts the formation of an even stronger free-surface vortex whose core, at times, penetrates inside the pump column and entrains air. The effects of decreasing submergence and increasing discharge on the mean position, strength and general structure of the main submerged vortices are discussed. DES results for Case 3 are also used to describe the dynamics of the main pump-bay vortices. Results also show that the differences between the DES and URANS predictions of the mean-flow vortical structure increase dramatically for Case 3. Despite large deformations of the free surface, no well-defined free-surface vortex is present in the URANS.