The non-linear interactions between large-scale momentum regions and small-scale structures induced by the presence of the roughness have been studied in boundary layers consisting of staggered cube arrays with plan area packing density of 6.25%, 25% or 44.4%. The measurements, consisting of hot-wire anemometry, were conducted at two Reynolds numbers in each of the canopy configurations. The canopy configuration is shown to have a significant influence on all parameters of the predictive model close to the roughness elements which is a result of the characteristics of the small-scale structures induced by the presence of the cubes. Several tests of the predictive model have been undertaken, demonstrating the good capability of the model to reproduce accurately spectra and statistics up to the 4th order. The model must be however calibrated for each type of canopy flow regime.