Highly heterogeneous floodplains can give rise to secondary flow structures responsible for the bulk of lateral momentum exchange. Quantifying the redistribution of momentum is required to predict lateral profiles of flow velocity and the associated water level in a river. In the work herein, we focus on studying secondary flow structures and the momentum redistribution associated with a lateral bed-roughness variation in a channel with low relative submergence of the roughness elements, h/k = 3, 2 and 1.5, where h is the flow depth and k is the roughness height. A series of laboratory experiments were performed in a flume containing rows of cubes. They were arranged in two types of regular patterns, with higher and lower frontal density, and placed side by side such that the bed roughness varies in the lateral direction. The measurements were performed using stereoscopic PIV in a vertical cross plane spanning between the two roughness types. The time-averaged and turbulence statistics of the three components of the velocity field were analyzed. First, we focus on the intensity of the secondary currents. As the flow becomes shallower (lower relative submergence), the cross-stream velocity normalized by the streamwise velocity increases. ... mehrA large-scale secondary current at the border between the two roughnesses as observed in  (though in their case between smooth and rough regions) appears for h/k = 3. As h/k decreases, this structure reaches to the same size as the secondary flow generated by the roughness elements. Also, the discharge distribution between the two sides of the channel becomes less uniform with decreasing h/k. In this sense, the relative importance of the roughness difference increases with decreasing water depth. Moreover, higher discharge is observed on the side with higher equivalent sand roughness, contrary to what is observed for smooth-to-rough transition [1, 2]. Time series of the streamwise velocity fluctuations are calculated using Taylor’s “frozen turbulence” hypothesis. In this representation, streamwise velocity streaks are apparent for h/k = 3, but they appear to lose coherence for the most shallow case of h/k=1.5.