Glassy polymers are often used for gas separations because of their high selectivity. Although the dual-mode permeation model correctly fits their sorption and permeation isotherms, its physical interpretation is disputed, and it does not describe permeation far from steady state, a condition expected when separations involve intermittent renewable energy sources. To develop a more comprehensive permeation model, we combine experiment, molecular dynamics, and multiscale reaction–diffusion modeling to characterize the time-dependent permeation of N2 and CO2 through a glassy poly(dimethyl phenylene oxide) membrane, a model system. Simulations of experimental time-dependent permeation data for both gases in the presteady-state and steady-state regimes show that both single- and dual-mode reaction–diffusion models reproduce the experimental observations, and that sorbed gas concentrations lag the external pressure rise. The results point to environment-sensitive diffusion coefficients as a vital characteristic of transport in glassy polymers.