Zeolites are microporous metal aluminosilicates widely used to remove heavy metal cations from contaminated waters through ion exchange. Experimental observations have shown that the cation exchange capacities of zeolites can be well described by the Freundlich isotherm with fitting parameters regulated by solution pH and ion specificity; however, quantitative relationships have not been established, indicating a lack of understanding for the underlying mechanisms of zeolite cation exchange. Here, we present a novel physical model to relate proton concentration and ion energetics to the Freundlich parameters and thus elucidate the underlying mechanisms of pH control and ion specificity. The physical model is developed by considering capillarity in zeolite cation exchange, instead of the homogeneous equilibrium that has previously used to understand cation exchange, which leads to the Freundlich isotherm, instead of the Langmuir isotherm often used in data analysis. Using the Freundlich power and equilibrium constant, we further show that the pH dependence of cation exchange capacity can be quantitatively explained by the change of proton chemical potential. At pH 7 under which proton does not significantly affect the cation exchange, the comparison of Freundlich power and equilibrium constant among different metal cations reveals grouping according to their electronic structures.