Self-assembled monolayers (SAMs) have become a standard tool for exploring surface interactions. Although well characterized, SAMs are known to undergo structural and conformational changes in the presence of solution, yet the ability to quantify these changes remains an obstacle due to limited analytical techniques. In this study, we determine changes in structure and conformation of CH3, OH, and COOH terminated hexadecanethiols on gold in water by means of a new technique known as evanescence reflection spectroscopy. This FTIR application, in conjunction with a semiempirical formalism, is capable of providing both qualitative and quantitative understanding of the molecular structure and orientation at the solid/liquid interface.