In this study, macro-rough flows over beds with different permeability values are simulated using the large-eddy simulation, and the results are analysed by applying the double-averaging (DA) methodology. Spheres of different sizes and arrangements were used to form the beds, which are deemed to be permeable granular beds. The influence of bed permeability on the turbulence dynamics and structure is investigated. It was observed that the scales of the spanwise vortical structures over more permeable beds are larger than those over less permeable beds. This is attributed to large-scale spanwise-alternate strips of varying Reynolds shear stress (RSS), emerging from the surface of macro-rough elements for the permeable beds. The DA stress balance suggests that the time-averaged spanwise vortical structure leads to a damping in DA RSS and an unusual peak of the form-induced stress in the main flow. In the streamwise direction, both large turbulent structures that originate from the Kelvin–Helmholtz-type instability and small turbulent structures that are associated with the turbulent transport across the gaps of the roughness elements are more prevalent over highly permeable beds. Near the bed, the relative magnitude of turbulent events shows a transition from a ejections-dominating to sweeps-dominating zone with vertical distance. Further, several hydrodynamic characteristics normalized by inner scales (kinematic viscosity to shear velocity ratio) show a greater dependency on permeability Reynolds number than those normalized by sediment size. The study provides an insight into the mechanism of mass transfer near the fluid–particle interface, which is vital to benthic and aquatic ecology.