In this work, we studied the influence of the thickness of plasmonic nanostructures composed of gold nanoparticles on the intensity of lines in SERS spectra of methylene blue (MB), 1,2 bis(4 pyridyl)ethylene (BPE), and malachite green (MG) used as analytes. Plasmonic nanostructures were patterned on alumina substrates by dry aerosol printing with spark discharge synthesized gold nanoparticles (mean size 9.5 nm) and represented layers 3 mm × 3 mm in size with the thickness of about 0.3, 0.4, and 0.5 μm. The enhancement factor was estimated at 5.5×106 for MB, 8.0×106 for BPE, and 2.1×107 for MG by using SERS spectra measured on nanostructures with the optimal thickness of 0.4 μm.