Atomic force microscopy (AFM) can be used to measure surface properties at the nanoscale. However, interpretation of measurements from amplitude modulation AFM (AM-AFM) in liquid is not straightforward due to the interactions between the AFM tip, the surface being imaged, and the water. In this work, amplitude-distance measurements and molecular dynamics simulations of AM-AFM were employed to study the effect of surface chemistry on the amplitude of tip oscillation in water. The sample surfaces consisted of self-assembled monolayers where the hydrophilicity or hydrophobicity was determined by the terminal group of the alkanethiols. Analysis showed that surface chemical composition influences the hydration structure near the interface which affects the forces experienced by the tip and in turn changes the amplitude profile. This observation could aid our understanding of AM-AFM measurements of interfacial phenomena on various surfaces in water.