<p>Structure and dynamics of turbulent open channel flow over permeable and impermeable sediment beds are investigated using pore-resolved, direct numerical simulations. Time-space double-averaged statistics are computed in four configurations: (i) permeable bed with randomly packed sediment grains, (ii) an impermeable wall with full layer of roughness elements matching the top layer of the sediment bed, (iii) an impermeable wall with half layer of roughness elements, and (iv) a smooth wall. It is observed that the mean velocity, Reynolds stresses, and form-induced pressure–velocity correlations representing ejection and sweep fluxes are similar in magnitude for the permeable-bed and impermeable full-layer cases. The wall-blocking effect present in the impermeable half layer results in higher streamwise and lower wall-normal stresses compared to the permeable bed. Bed roughness increases Reynolds shear stress, whereas permeability has minimal influence. However, bed permeability significantly influences form-induced shear stress. Pressure fluctuations and volume-averaged bed-normal distribution of the drag force peak in the top layer of the bed. These findings suggest that reach-scale transport in the hyporheic zone will be better captured by providing boundary conditions based on stream flow simulations that incorporate the roughness effect of the top layer of the bed.</p>