Presented herein is a combined experimental and computational study of the gold nanoparticle (AuNP) inner filter effect on surface enhanced Raman spectroscopic (SERS) measurements. Using a bianalyte strategy in which dithiopurine (DTP) and ethanol were employed as the model analytes, we demonstrated that AuNPs enhance DTP's Raman signal but attenuate ethanol's Raman intensity. Combined time-resolved UV-vis and Raman measurements showed that AuNP aggregation has significant and an exactly opposite impact on the AuNP inner filter effect and SERS enhancement. This research provides critical new insights regarding SERS signal variation and offers a simple methodology for reliable determination of the SERS enhancement factors.