The adsorption energies of perfluorobutanesulfonic acid, perfluorobutanoic acid, and trifluoroacetic acid on functionalized activated carbon are calculated from first principles. We introduce a novel approach based on a thermochemical cycle and a continuum solvation model to address neutral and charged adsorption complexes and account for concentration, pH, and pore-size effects. The results highlight the benefit of N-based functional groups for enhancing the removal of challenging, short-chain perfluoroalkyl substances from water by activated carbon.