Gold nanostructures (AuNSs) were used to fabricate surface-enhanced Raman spectroscopy (SERS) substrates. These AuNSs were produced by the solid-state dewetting method from thin films. The fragmentation process was studied at 300 °C, considering the duration of the thermal treatment for 1, 3, 6, and 12 hours. These SERS substrates were then employed to detect Rhodamine B (RhB) as a model analyte, simulating a contaminant in water at a concentration of 5 ppm. The morphology of the AuNSs was examined using SEM, which revealed a spheroidal shape beginning to coalesce after 12 hours. The size of the AuNSs was estimated to range from 22 ± 7 to 24 ± 6 nm, depending on the annealing time. The surface plasmon resonance of the AuNSs was determined using absorption spectroscopy, showing a shift as the annealing time increased. The SERS signals of RhB adsorbed on the AuNS substrates were studied, and a comparative analysis showed no significant differences in the positions of the bands; however, variations in intensity enhancement ranged from 20 to 90 times for 6 and 3 hours, respectively. Three new vibrational modes, observed at 1683, 1720, and 1789 cm–1, have been identified and reported.