Clays and micas are receiving attention as materials that, in their atomically thin form, could allow for novel proton conductive, ion selective, osmotic power generation, or solvent filtration membranes. The interest arises from the possibility of controlling their properties by exchanging ions in the crystal lattice. However, the ion exchange process itself remains largely unexplored in atomically thin materials. Here we use atomic-resolution scanning transmission electron microscopy to study the dynamics of the process and reveal the binding sites of individual ions in atomically thin and artificially restacked clays and micas. Imaging ion exchange after different exposure time and for different crystal thicknesses, we find that the ion diffusion constant, D, for the interlayer space of atomically thin samples is up to 10^4 times larger than in bulk crystals and approaches its value in free water. Surprisingly, samples where no bulk exchange is expected display fast exchange if the mica layers are twisted and restacked; but in this case, the exchanged ions arrange in islands controlled by the moire superlattice dimensions. We attribute the fast ion diffusion to enhanced interlayer expandability resulting from weaker interlayer binding forces in both atomically thin and restacked materials. Finally, we demonstrate images of individual surface cations for these materials, which had remained elusive in previous studies. This work provides atomic scale insights into ion diffusion in highly confined spaces and suggests strategies to design novel exfoliated clays membranes.