The structure of small gold nanoclusters (around 2.5 nm) deposited on different silica-on-silicon (SiOx/Si) substrates is investigated using several characterization techniques (AFM, XRD, EXAFS and GISAXS). The grain morphology and the surface roughness of the deposited gold cluster layers are determined by AFM. The in-plane GISAXS intensity is modelled in order to obtain information about the cluster size and the characteristic length scale of the surface roughness. The surface morphology of the deposited clusters depends on whether the native defect-rich (n-SiOx/Si) or the defect-poor substrate obtained by thermal treatment (t-SiO2/Si) is used. Gold clusters show a stronger tendency to aggregate when deposited on n-SiOx/Si, resulting in films characterized by a larger grain dimension (around 20 nm) and by a higher surface roughness (up to 5 nm). The more noticeable cluster aggregation on n-SiOx/Si substrates is explained in terms of metal-support interaction mediated by the defects located on the surface of the native silica substrate. Evidence of metal-support interaction is provided by EXAFS, demonstrating the existence of an Au-O distance for clusters deposited on n-SiOx/Si that is not found on t-SiO2/Si.