Proton dissociation and transfer are investigated with ab initio molecular dynamics (AIMD) simulations of carbon nanotubes (CNT) functionalized with perfluorosulfonic acid (-CF2SO3H) groups with 3 H2O/–SO3H. The CNT systems were constructed both with and without fluorine atoms covalently bound to the inner walls to determine the effects of the presence of fluorine on proton dissociation, hydration, and stabilization. The results of the AIMD trajectories show that decreasing the separation of sulfonic acid groups increases the propensity for proton dissociation. The simulations also revealed that the dissociated proton was preferentially stabilized as a hydrated hydronium (H3O+) cation in the CNT systems with the fluorine. This feature is attributed to the fluorine atoms providing a localized negative charge that promotes hydrogen bonding of the water molecules coordinated to the central hydronium ion. The hydrated H3O+ ion differed from a traditional Eigen cation (H9O4 +) as it donated hydrogen bonds to sulfonate oxygen atoms, as well as water molecules.