Pore-resolved direct numerical simulations have been performed to investigate the turbulent open-channel flow over a rough and permeable sediment bed, represented by a mono-disperse random sphere pack. After a careful validation, eleven cases were simulated to systemically sample a parameter space spanned by a friction Reynolds number $Re_\tau \in [150, 500]$ and a permeability Reynolds number $Re_K \in [0, 2.8]$. By varying the ratio of flow depth to sphere diameter within a range of $h/D \in \{ 3,5,10,\infty \}$, the influence of both Reynolds numbers on the flow field and the turbulence structure could be investigated independently. The simulation results are analysed within a time–space double-averaging framework, whereas flow visualizations provide insight into instantaneous fields. Based on the drag distribution, we propose a consistent interface description, which can be used to define both near-interface and outer-flow coordinates. In these near-interface coordinates, the profiles of the mean velocity and the total shear stress collapse. Furthermore, the proposed interface definition yields outer-layer coordinates, in which the flow and turbulence statistics over a rough and permeable bed reveal similarity to a smooth-wall flow at a similar $Re_\tau$. Within the parameter space, $Re_\tau$ has a strong influence on the wake region of the velocity profile. In contrast, $Re_K$ changes the wall-blocking effect and the shear intensity, which is reflected by the turbulence structure and vortex orientation in the near-interface region. As streamwise velocity streaks disappear and the vortex inclination increases with higher $Re_K$, differences between near-interface and outer-layer turbulence structure are reduced.