This paper presents the results of a LES of turbulent surface jets over a submerged weir. The mean flow and turbulent structures are presented for both flat and deformed bed conditions. LES results with the scour hole reveal that the separated shear layer is extended by about three times, locating the reattachment point further downstream. In addition, the presence of the scour hole increases both total and maximum TKE and decreases near-bed TKE. Quantitatively, with the scour hole, the maximum near-bed TKE is decreased by 50%. It turns out that the area of high instantaneous bed shear stress does not match with that of high time-averaged bed shear stress, but does match well with that of the high near-bed TKE. The vortices generated by the weir propagate differently with and without the scour hole and shed light on the generating mechanism of a scour hole.