SERS substrates fabricated from chemically synthesized nanoparticles (NPs) offer a distinct advantage of localizing and enhancing the electromagnetic fields by facile tuning of NP size, shape and interparticle distances. In this report, two-dimensional arrays of micrometre-sized clusters of gold nanoparticles protected by (i) sodium citrate and (ii) tris(2,4-dimethyl-5-sulfonatophenyl)phosphine (TDSP) ligands were directly assembled from colloidal suspensions onto flat, non-patterned substrates by discontinuous ('Stop&Go') convective self-assembly. The micrometric spacing between the NP clusters makes it easy to address them individually by confocal Raman microscopy. The packing of the gold NPs within these clusters with interparticle spacings of the order of nanometres leads to an optical response dominated by coupled surface plasmon resonances, and favours a strong enhancement of electromagnetic fields useful for surface enhanced Raman scattering (SERS). These NP clusters make very uniform SERS substrates, with reproducible SERS responses from cluster to cluster. The potential of these NP clusters for optical biosensing is demonstrated by the SERS detection of a biologically relevant molecule, cytosine, adsorbed onto the NP clusters. The presented results are promising for designing an original class of nanoparticle-based SERS microarrays. The new paradigm of convective self-assembly could be exploited generally for the patterning of various other types of colloidal micro- and nano-objects, such as semiconducting NPs, magnetic NPs, bacteria or proteins.