Glass beads were used to model permeable beds and boulders (simulated by plastic spherical balls) placed on the centre section of the bed. Flume experiments were conducted to investigate the hydrodynamics through a boulder array over impermeable and permeable beds (i.e. IMPB and PB). For background reference, hydrodynamics investigation has been made over smooth beds (SB) with the boulder array. Through measuring the instantaneous velocity field, the major flow characteristics such as mean flow velocity, turbulence intensity, turbulent kinetic energy (TKE) and instantaneous Reynolds stresses (through quadrant analysis). The results show that the increase in bed permeability through decreasing the exposure height of boulders has a little impact on the magnitude of streamwise velocity, but tends to decrease the near-bed velocity gradient, thus affecting the bed shear stress. For turbulence, similar to the previous studies, the bed permeability is identified to enable the downward shift the peak of turbulence intensity. The TKE budget analysis shows that bed permeability tends to inhibit transport and diffusion processes of the TKE generation. Finally, the quadrant analysis of turbulence structure clearly shows that the ejections (Q2) and sweeps (Q4) with and without the boulder array are dominated by the turbulence structure of different scales.