Surface-enhanced Raman spectroscopy (SERS)-based biosensors have recently been extensively developed because of their high sensitivity and non-destructive nature. Conventional SERS substrates are unsuitable for detecting biomolecules directly from human skin. As a result, significant effort is being put into developing a gel-type SERS sensor that can segregate and detect biomolecules due to differences in molecular transport phenomena in the gel. However, no comprehensive research studies on the transport processes of molecules in gels in gel-type SERS sensors have been reported. This paper reports the differences in the transport phenomena of different molecules based on the time change of SERS spectrum intensity. The Au nanorod array substrate was coated with HEC gel to prepare a sample cell to study diffusion. The SERS spectra of aqueous solutions of 9 types of molecules were measured using the prepared sample cells. The rate at which each molecule diffuses into the gel differs depending on the molecule. The time variation of the characteristic SERS peak of each molecule was investigated based on a one-dimensional diffusion model, and the diffusion coefficient D was calculated for each molecule. A comparative study was conducted on the relationship between the diffusion coefficient and the molecular weight and molecular size, and it was found that the larger the molecular weight and molecular size, the slower the diffusion, which is based on the molecular motion theory and the inhibitory effect of the gel substance.