Large-eddy simulations (LES) of the flow over a non-uniformly roughened channel bed are carried out to study the effect of non-uniform bed roughness on turbulence driven secondary currents and turbulence statistics. The channel bed is comprised of alternating rough and smooth strips, the width of which corresponds to the water depth. The Reynolds number based on hydraulic radius and bulk velocity is 34,000. The LES are successfully validated using experimental data. The secondary flow and bed roughness have a significant effect on the streamwise velocity and second order turbulence statistics. Turbulence is enhanced over rough strips and suppressed over smooth strips. Significant lateral momentum transfer takes place due to both advection and turbulence. The bed shear stresses over the smooth strips are approximately four times less than over the rough strips a result of near bed low momentum fluid being transported from the rough strips to the smooth strips and high momentum fluid being convected from the surface towards the bed. The most significant terms in the streamwise momentum equation are quantified and discussed with regard to momentum transfer.