Quantifying turbulent fluxes and secondary structures in shallow channel flows is important for predicting momentum and mass transfer in rivers as well as channel capacity and associated water levels. Here, we focus on the flow over a lateral bed-roughness variation with very low relative submergence of the roughness elements, h∕k ={3, 2, 1.5}, where h is the flow depth and k is the roughness height. Measurements were performed in a 1.1 m wide and 26 m long glass flume whose bed was fitted with cubes arranged in two regular side-by-side patterns with frontal densities λf = 0.2 and 0.4 to create a rough-to-rougher variation. Measurements were performed using stereoscopic PIV in two orthogonal planes, in a vertical transverse plane spanning the two roughness types, and in a longitudinal one at the interface between the roughness types. The results show that the bulk velocity difference between the two sides of the channel increases with decreasing h/k. Also, contrary to what is observed at high relative submergence with smooth-to-rough transitions, higher bulk velocities occur on the side with higher roughness. This difference is increasing as the flow becomes shallower and is shown to be due to increasing effective depths ratios, leading to increasingly lower friction factor ratios with lower friction factors on the high-velocity but rougher side. Although increasing streamwise momentum transfer at the interface is needed as h/k decreases, the turbulent and secondary circulation transfer of momentum is increasingly inhibited. A globally-driven secondary-circulation at h∕k = 3 ceases for lower h/k and roughness-scale circulation becomes dominant. Also, even the increased global shear does not lead to large-scale Kelvin Helmholtz instabilities structures. However, the relative importance of the roughness difference on the flow is augmented as the flow becomes shallower and momentum transfer due to lateral dispersive stresses increases.