This dataset contains raw spectral data associated with the main figures in a publication detailing a new thin-film multi-layer gold nanoparticle aggregate ('MLagg') surface-enhanced Raman spectroscopy (SERS) substrate. SERS and dark-field (DF) scattering measurements were collected by mapping spectra across the substrate surface. The DF data is referenced to a white light scattering target and has been background subtracted to remove dark counts. The dataset characterises the MLagg substrate, demonstrates surface cleaning and functionalisation control methods, as well as the substrate's application for in-flow sensing of paracetamol and detection of vapours such as toluene.