The ubiquitous CLC membrane transporters are the only transporter family known to exchange anions for cations. Despite extensive study, there is no model to completely explain the 2:1 Cl‒/H+ stoichiometric exchange mechanism. Here, we provide such a model. Using CLC-ec1, a bacterial homolog that has served as a paradigm for the family, we determined cryo-EM structures at pH 7, pH 4.5, and pH 3. Molecular dynamics simulations of the pH-3 structure reveal critical steps in the transport mechanism, including release of Cl- ions to the extracellular side, opening of the inner gate, and water wires that facilitate H+ transport. Water wires are observed frequently in both the canonical H+-transport pathway and in the Cl- pathway, where they had not been previously reported. We propose that tight coupling of Cl‒/H+ transport is maintained (uncoupled H+ transport is avoided) because H+ transfer from the water wires to the catalytic glutamate is favored only when Cl‒ is also present in the pathway . Mutations that weaken Cl‒ binding without changing the pathway structure exhibit functional properties consistent with this model.