Two-dimensional (2D) materials such as graphene, molybdenum sulfide, and hexagonal boron nitride are widely studied for separation applications such as water desalination. Desalination across such 2D nanoporous membranes is largely influenced by the bulk transport properties of water, which are, in turn, sensitive to the operating temperature. However, there have been no studies on the effect of temperature on desalination through 2D nanopores. We investigated water desalination through hydrogen functionalized graphene nanopores of varying pore areas at temperatures 275.0 K, 300.0 K, 325.0 K, and 350.0 K. The water flux showed a direct relation with the diffusion coefficient and an inverse relation with the hydrogen-bond lifetime. As a direct consequence, the water flux was found to be related to the temperature as per the Arrhenius equation, similar to an activated process. The results from the present study improve the understanding on water and ion permeation across nanoporous 2D materials at different temperatures. Furthermore, the present investigation suggests a kinetic model, which can predict the water and ion permeation based on the characteristics of the nanopore. © 2020 American Institute of Physics Inc.. All rights reserved.