Integrating functionalized 2D materials into multilayer device architectures increasingly requires an understanding of the behavior of noncovalently adsorbed ligands during solution and thermal processing conditions. One common functionalization approach involves assembly of alkynoic acids with an internal diyne on HOPG or graphene, forming a lying down phase monolayer in epitaxy with the substrate, that can then be photopolymerized to enhance robustness. Using a combination of contact angle titrations and molecular dynamics simulations, we demonstrate that headgroup dynamics and tail-substrate interactions can be altered by changing the position of the internal diyne or the length of the fatty acid, thereby modulating wettability of the 2D material. Molecules with short chain segments proximal to the carboxylic acid head undergo significant dynamics after polymerization, allowing the headgroups to interact more readily with solvents and increasing hydrophilicity. For specific terminal alkyl segment lengths, we instead observed a decrease in hydrophilicity of the monolayer post-polymerization, suggesting chain-length specific differences in the polymerization. Together, these observations enable us to selectively control the surface chemistry of the 2D material to create desired interactions with the environment.