Ion exchange in nanoporous clay-rich media plays an integral role in water, nutrient, and contaminant storage and transport. In montmorillonite (MMT), a common clay mineral in soils, sediments, and muds, the swelling and collapse of clay particles through the addition or removal of discrete molecular layers of water alters cation exchange selectivities in a poorly understood way. Here, we show that ion exchange is coupled to the dynamic delamination and restacking of clay layers, which creates a feedback between the hydration state of the exchanging cation and the composition of the clay interlayer. Particles with different hydration states are distinct phases with unique binding selectivities. Surprisingly, equilibrium achieved through thermal fluctuations in cation concentration and hydration state leads to the exchange of both ions and individual MMT layers between particles, a process we image directly with high-resolution transmission electron microscopy at cryogenic conditions (cryo-TEM). We introduce an exchange model that accounts for the binding selectivities of different phases, which is likely applicable to many charged colloidal or macromolecular systems in which the structural conformation is correlated with the activities of water and counterions within spatially confined compartments.