A laboratory study is reported on the flow perturbations induced by a cylinder across an open-channel flow at a subcritical Reynolds number of 〖Re〗_D=〖10〗^4 (based on the cylinder diameter). Inspired by field measurements on the Plizska River, Poland, the investigated configuration is representative of large wood trunks that traverse a river. The flow perturbation induced by cylinders has been abundantly investigated in infinite unbounded configurations. Surprisingly, cylinders placed in a bottom boundary layer, such as found in rivers, have hardly been investigated. A first aim is to analyze the flow perturbations induced by the cylinder, such as the half-width of the wake, the velocity deficit, the decay of the perturbations in velocity, turbulent kinetic energy and Reynolds stresses. A second aim is to analyze the effect of the bed boundary layer on the perturbations induced by the cylinder, and the effect of the latter on the bed boundary layer. This is important as it can have implications on the morphology, the hyporheic exchanges and the biota. That can also be observed by looking at the differences between two different frameworks: absolute and relative. The study reveals that important differences exist between the flow perturbations in unbounded and bounded configurations, and provides guidelines for the quantification of these flow perturbations in rivers.