Abstract The ubiquitous existence of water confined in nano-capillaries is key to fundamental biological and technological applications. Using molecular dynamics simulations, we analyzed the hopping-like interlayer relocation dynamics of bilayer water confined between two parallel graphene sheets. In contrary to the common scheme that relocation is driven by density fluctuations, analysis of the transition path ensemble revealed that interlayer hopping is induced by local hydrogen bond configuration fluctuations coupled with activated consecutive transient angular reorientations. Our results consolidated the anisotropic nature of water relocation under strong ordering, which provided a mechanistic insight into the relaxation behavior at glass-forming water’s fragile-to-strong crossover.