We show how a two-state diffusion-reaction description of the mobility of ions confined within compacted clays can be constructed from the microscopic dynamics of ions in an external field. The diffusion-reaction picture provides the usual interpretation of the reduced ionic mobility in clays, but the required partitioning coefficient Kd between trapped and mobile ions is generally an empirical parameter. We demonstrate that it is possible to obtain Kd from the microscopic dynamics of ions interacting with the clay surfaces by evaluating the ionic mobility using a novel lattice implementation of the Fokker-Planck equation. The resulting Kd allows a clear-cut characterization of the trapping sites on the clay surfaces and determines the adsorption/desorption rates. The results highlight the limitations of standard approximation schemes and pinpoint the crossover from jump to Brownian diffusion regimes.