In mountainous rivers, large relatively immobile grains partly control the local and reach-averaged flow hydraulics and sediment fluxes. When the flow depth in low relative submergence conditions plunging flow and the highly three-dimensional flow field can cause spatial distributions of bed surface elevations and grain size distributions, therefore, causing a spatially variable sediment transport rate. We conducted a set of experiments to study how the bed surface responds to this spatial variability and in particular the effect relative submergence in the formation of sediment patches around simulated large boulders. Same average sediment transport capacity, upstream sediment supply, and initial bed thickness and grain size distribution were imposed in all experiments. The detailed flow field around the boulders was obtained using a combination of laboratory measurements and a 3D flow model based on the Volume of Fluid technique. The local shear stress field displayed substantial variability and controlled the bedload transport rates and direction in which sediment moved. The divergence in shear stress caused by the hemispheres promoted size-selective bedload deposition, which formed patches of coarse sediment upstream of the hemisphere. Sediment deposition caused a decrease in local shear stress, which combined with the coarser grain size, enhanced the stability of this patch. The region downstream of the hemispheres was largely controlled by a recirculation zone and had little to no change in grain size, bed elevation, and shear stress. The formation, development and stability of sediment patches in mountain streams is controlled by the shear stress divergence and magnitude and direction of the local shear stress field.