Honami and monami waves are caused by large-scale coherent vortex structures which form in shear layers generated by canopies. In order to reach new insights on the onset of such waves, the instability of these shear layers is studied. Two different approaches are used. In the first approach, the presence of the canopy is modeled via a drag coefficient, taken to vary along the canopy as by experimental indications. The second approach considers the canopy as a porous medium and different governing equations for the fluid flow are deduced. In this second case, the anisotropy of the canopy, composed by rigid cylindrical elements, is accounted for via an apparent permeability tensor. The results obtained with the latter approach approximate better experimental correlations for the synchronous oscillations of the canopy.