The effect of pH and layer charge on the swelling, migration of clay particles, and resulting permeability reduction due to changes in salt concentration has been studied. Porous media containing swelling clays exhibit a drastic decrease in permeability when subjected to salinity changes under acidic conditions. Experiments suggest that this reduction in permeability is caused by macroscopic swelling and release of clay aggregates. The critical salt concentration of sodium chloride at which the transition from crystalline to osmotic swelling regimes occurs is shown to be independent of pH for Wyoming montmorillonite. The layer charge of the clays is also shown to influence the critical salt concentration at which the transition occurs. A 30% reduction in layer charge of Wyoming montmorillonite is sufficient to collapse the clays irreversibly. These effects of pH and layer charge on the critical salt concentration are explained using a surface complex model that predicts the diffuse layer charge as a function of the surface charge, ionic strength, pH, and the affinity of the counterions to the surface. This model can be extended to predict the diffuse layer charge and the critical salt concentration in multicomponent solutions to provide a predictive tool for preventing permeability reduction in porous media containing swelling clays.