Spatial heterogeneity of flows over rough permeable and impermeable gravel-bed streams is experimentally quantified in a laboratory flume and characterised by form-induced shear stresses. To create the rough bed stream, uniform gravel is laid down in five layers. This will ensure that the stream bed is properly prepared and has the desired texture and permeability, while its impermeable counterpart is prepared by casting the permeable gravel-bed with synthetic resin within the working area. For the instantaneous velocity measurement, a three-dimensional ADV (Acoustic Doppler velocimeter) was used. For data analysis, the double-averaging (DA) methodology was applied. Higher flow penetration depth in permeable gravel-bed stream induces organized flow turbulence and damping of DA Reynolds shear stresses (DA RSS). Importantly, the wall-blocking in resin casted gravel-bed stream prevented fluid infiltration leading to shifting of linear stress profile towards the free surface zone. DA FISS contributed significantly to the DA RSS near the mean bed level and attributed to higher spatial velocity fluctuations. The comparative study of DA TKE-flux shows that the TKE-fluxes are larger in permeable gravel-bed stream and attributed to higher spatial flow heterogeneity.