Turbulent flows in rough open-channels have complex structures near the channel-bed. The near-bed flow can cause bed erosion, channel instability, and damages to fish habitats. This paper aims to improve our understanding of the structures. Transverse square bars placed at the channel-bed form two-dimensional roughness elements. Turbulent flows over the bars are predicted using large eddy simulation (LES). The predicted flow quantities compare well with experimental data. The LES model predicts mean-flow velocity profiles that resemble those in the classic turbulent boundary layer over a flat plate and profiles that change patterns in the vicinity of roughness elements, depending on the pitch-to-roughness height ratio λ/k. The relative turbulence intensity and normalized Reynolds shear stress reach maxima of 15% and 1.2%, respectively, at λ/k = 8, compared to 9% and 0.2% at λ/k = 2. The predicted bottom boundary layers constitute a large portion of the total depth, indicating roughness effect on the flow throughout the water column. Fluid exchange between the roughness cavity and outer region occurs due to turbulence fluctuations. The fluctuations increase in intensity with increasing λ/k ratio. This ratio dictates the number of eddies in the cavity as well as their locations and shapes. It also controls turbulence stress distributions. LES can be used to explore strategies for erosion control, channel restoration, and habitat protection.