The influence of graphene oxide supports and thiolate surface ligands on the catalytic activity of colloidal Pd nanoparticles for alkyne hydrogenation in water is investigated. The studies show that unsupported, water-soluble thiolate-capped Pd nanoparticle catalysts favor the semi-hydrogenation over full-hydrogenation of dimethyl acetylene dicarboxylate (DMAD) under the atmospheric pressure and at room temperature. Pd nanoparticles supported on graphene oxide exhibit a similar activity for the hydrogenation of DMAD, but they show an improved long-term colloidal stability in aqueous solution after multiple catalytic cycles. After the heat treatment of Pd nanoparticles supported on graphene oxide at 300 °C, these heated hybrids exhibit an enhanced catalytic activity towards the full-hydrogenation. Overall, the studies suggest some influences of graphene oxide supports on the stability and thiolate surface ligands on the activity and selectivity of Pd nanoparticle catalysts.