The distinctive sediment bed morphology modulated by the wake flow of a wall-mounted deformable plate across various structural aspect ratio and incoming flow speeds was investigated experimentally in a water channel. A surface scanner was implemented to quantify bed topography, and a tomographic particle image velocimetry system was used to characterize the three-dimensional wake flows. Results show that due to the deflection of incoming flow, the velocity magnitude enhanced at lateral sides of the plate, which produced distinctive scour holes in these regions. The level of velocity magnitude enhancement was highly correlated to postures of deformable plate. At a given flow speed, plate with lower aspect ratio exhibited smaller deformation, which produced more distinctive near-bed velocity enhancement in wake deflection zone and therefore led to higher erosion volume. Further inspection indicated that when deformation of the plate was small, the larger velocity enhancement close to bed can be attributed to higher plate drag coefficient and stronger flow mixing with high momentum flows away from bed. Supported with measurements, a basic formulation was established to quantify the shear stress acting on sedimentary bed as a function of incoming flow speed and plate aspect ratio.