Poly(dimethylsiloxane) (PDMS) materials have been extensively shown to function as excellent fouling-release (FR) coatings in the marine environment. The incorporation of biocide moieties, such as quaternary ammonium salts (QAS), can impart additional antibiofouling properties to PDMS-based FR coating systems. In this study, the molecular surface structures of two different types of QAS-incorporated PDMS systems were investigated in different chemical environments using sum frequency generation vibrational spectroscopy (SFG). Specifically, a series of PDMS coatings containing either a QAS with a single ammonium salt group per molecule or a quaternary ammonium-functionalized polyhedral oligomeric silsesquioxane (Q-POSS) were measured with SFG in air, water, and artificial seawater (ASW) to investigate the relationships between the interfacial surface structures of these materials and their antifouling properties. Although previous studies have shown that the above-mentioned materials are promising contact-active antifouling coatings, slight variations of the QAS structure can lead to substantial differences in the antifouling performance. Indeed, the SFG results presented here indicated that the surface structures of these materials depend on several factors, such as the extent of quaternization, the molecular weight of the PDMS component, and the functional groups of the QAS used for incorporation into the PDMS matrix. It was concluded that in aqueous environments a lower extent of Q-POSS quaternization and the use of ethoxy (instead of methoxy) functional groups for QAS incorporation facilitated the extension of the alkyl chains away from the nitrogen atom of the QAS on the surface. The SFG results correlated well with the antifouling activity studies that indicated that the coatings exhibiting a lower concentration of longer alkyl chains protruding out of the surface can neutralize microorganisms more effectively, ultimately leading to better antifouling performance. Furthermore, the results of this study provide additional evidence that incorporated QAS exert their antimicrobial activity through a two-step interaction. The first step is the adsorption of the bacteria on the surface as a result of the electrostatic attraction between the negatively charged microorganisms and the positively charged QAS nitrogen atoms on the surface. The second step is the disruption of the cell membranes by the penetration of the QAS long, extended alkyl chains.