In steep rivers, sediment is often transported over immobile cobbles and boulders. Previous studies of such conditions have observed that the entrainment rate of the mobile sediment strongly depends on the level of protrusion of the immobile grains. Here experiments are conducted in a laboratory flume in order to quantify how different levels of protrusion of large aggregates above a fixed fine-sediment bed, modeled as a patch of hemispheres, modify the local hydrodynamics near the fine-sediment bed. Five protrusion levels defined by P = k∕R = {0%, 20%, 40%, 60%, 80%} were investigated, where k is the protrusion height and R the radius. For small protrusion (P = 20%), enhanced shear stress and turbulence intensity on the fine-sediment bed is observed as the mixing layer generated at the hemisphere top impacts the fine-sediment bed. Moreover, sweep events generated near the top of the hemispheres reach the fine-sediment bed. For large protrusions (P ≥ 60%), the mixing layer generated near the top of the hemispheres does not reach the fine grains with the consequence that the shear stress drops. The remaining turbulence near the fine-sediment bed, although enhanced by the wakes generated by the hemispherical caps, is quasi-isotropic. The transition between these two distinct near-bed flow regimes is found to be around P = 40%, corresponding to the protrusion levels observed by Grams and Wilcock (2014, https://doi.org/10.1002/2013JF002925) above which the erosion of fine sediment ceases.