Using atomic force microscopy, we investigated how the morphology of layer-by-layer deposited polyelectrolyte multilayers is influenced by the physical properties of the supporting substrate. The surface coverage of the assembly and its topography were found to be dependent on the dielectric permittivity of the substrate and the strength of the electrostatic interactions between polyanions and polycations. For poly(allylamine hydrochloride)/poly(styrene sulfonate) (PAH/PSS), a strongly interacting polyelectrolyte couple, no dependency of the surface morphology on the physical properties of the underlying substrate was observed. In contrast, the weakly interacting pair poly(L-lysine)/hyaluronic acid (PLL/HA) formed rapidly continuous, flat layers on substrates of low dielectric permittivity and inhomogeneous droplet-films on substrates of high dielectric permittivity. Variations in the dielectric permittivity account for changes in the image charges that are induced in the substrate. These changes influence the balance between repulsive electrostatic forces (and image forces) and attractive van der Waals interactions, and thus cause the differences in surface morphology. Differences in surface charge did not influence the morphology of the polyelectrolyte multilayers, but higher surface charge resulted in more polymeric material adsorbed on the surface. A comparison between (PLL/HA) multilayers with and without an initial layer of poly(ethyleneimine) (PEI) supports this hypothesis.