Nanoporous graphene promises extremely high flow rates in membrane separation applications owing to its single atom thickness. While sub-nanometer graphene pores are desirable for rejecting ions and small molecules, transport through larger graphene nanopores is relevant in nanofiltration applications and to leakage flow through membrane defects. The permeance of these pores is commonly estimated using continuum transport relationships in graphene membrane modeling, although errors are expected due to sub-continuum behavior that emerges for smaller nanopores. In this paper we perform molecular dynamics simulations to understand the departure of solute advection–diffusion through graphene nanopores from continuum theory. We find that the same diameter dependent effective pore thickness can be used to adjust continuum models for both the net flow rate and solute mass transfer rate to match simulations. The increased resistance to both modes of transport is attributed to reduced molecule mobility in the dense layers of fluid that form on either side of the graphene and within the pore. The results further indicate the extent of deviations from continuum solute mass transfer that can be expected through graphene nanopores, toward more accurate modeling of nanoporous atomically thin membranes.