In the present work we have investigated the relationships existing between the optical properties and the growth mechanism, microstructure and surface roughness of SnO2 and ZnO oxide films prepared by magnetron sputtering under conditions resembling those utilized in industry. Thin films of these oxides with different thicknesses were characterized by atomic force microscopy, glancing incidence X-ray diffraction (GIXRD), X-ray reflectometry and spectroscopic ellipsometry. The roughness evolution of the film properties (density, surface roughness and refraction index) as a function of their thickness has been evaluated within the concepts of the Dynamic Scaling Theory of thin film growth. Zinc oxide films were rougher than tin oxide films of similar thickness, indicating a different growing mechanism for the two materials. Silver was evaporated onto the surface of the two oxide thin films and its earlier stages of nucleation studied by background analysis of the X-ray photoemission spectra. A different nucleation mechanism was found depending on the nature of the oxide acting as substrate. The superior performance of the zinc oxide based low emissive coatings is related with a better wetting of silver on the surface of this oxide despite the comparatively lower roughness of the tin oxide layers.