The stepwise hydration of clay minerals has been observed repeatedly in studies, but the underlying mechanism remains unclear. Previous numerical studies confirmed the presence of one-water layer (1W) and two-water layer (2W) hydration states. However, the undisturbed transition between these hydration states has never been captured. Using molecular dynamics simulation, this study (i) simulated for the first time the free 1W–2W transition during clay hydration and (ii) identified the underlying mechanism to be the detachment of cations from the clay surface and the formation of a shell of water molecules around the cation. The swelling dynamics of clay was found to be affected by the clay charge, clay mineralogy, and counterions through complex cation–clay interactions, cation hydration capacity, and cation migration rate. © 2022 The Authors. Published by American Chemical Society