Water diffusion in nanopores has attracted considerable attention in the past decades. Recently the coupling between the vibration of pore walls and movement of confined water has been recognized to largely enhance diffusion. However, its impact on water diffusion in graphene oxide membranes remains to be discussed. Here we explore how water diffusion couples with the thermal fluctuation of graphene nanochannels by molecular dynamics simulations. Our finding demonstrates an approximately linear dependence of diffusion enhancement on temperature; i.e., the wiggling nanopore enhances diffusion at low temperature and inhibits diffusion at high temperature. This mechanism is further extended to be applicable for another two typical layered materials, hBN and MoS2. These results offer opportunities to tune surface diffusion by thermal operation or mechanical activation, advancing the application of two-dimensional materials in membrane separations.