Water filtration membranes with advanced ion selectivity are urgently needed for resource recovery and the production of clean drinking water. This work investigates the separation capabilities of cross-linked zwitterionic copolymer membranes, a self-assembled membrane system featuring subnanometer zwitterionic nanochannels. We demonstrate that selective zwitterion–anion interactions simultaneously control salt partitioning and diffusivity, with the permeabilities of NaClO4, NaI, NaBr, NaCl, NaF, and Na2SO4 spanning roughly three orders of magnitude over a wide range of feed concentrations. We model salt flux using a one-dimensional transport model based on the Maxwell–Stefan equations and show that diffusion is the dominant mode of transport for 1:1 sodium salts. Differences in zwitterion–Cl− and zwitterion–F− interactions granted these membranes with the ultrahigh Cl−/F− permselectivity (PCl-/PF- = 24), enabling high fluoride retention and high chloride passage even from saline mixtures of NaCl and NaF.