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Large eddy simulations (LES) of flow over wall-mounted boulders placed on a rough, permeable bed, composed of one layer of densely-packed spheres, are performed. This configuration is based on the experimental configuration reported in Papanicolaou et al. (2012) [14] the data of which are used to validate the LES. A fairly good agreement between calculated and measured time-averaged streamwise velocity and turbulence intensity profiles is found confirming the accuracy of the simulation. Details of the time-averaged and instantaneous flow are revealed using various visualisation methods. The time-averaged flow is characterised by a symmetric pair of funnel vortices comprising the recirculation zone in the lee of the boulder. The funnel vortex is bounded by significant shear layers caused by high-momentum fluid filling the low momentum wake zone behind the boulder. Bed roughness and permeability appears to play an important role in this flow, it affects the near-bed velocity profiles and subsurface fluid is entrained into the low pressure zone behind the boulder, specifically into the funnel vortex, moreover surface-subsurface flow exchange in particular in the vicinity of the boulders disrupts the secondary flow in the wake. The instantaneous flow features various turbulence structures which are educed by means of isosurfaces of the Q-criterion. Shear layer roll-up leads to high-frequency shedding of roller vortices, which are subsequently stretched by significant velocity gradients and deformed into a hairpin or horseshoe form. Vertical and horizontal shear layer flapping is revealed and quantified via vorticity contour plots and velocity spectra. [ABSTRACT FROM AUTHOR]