We present a numerical solution of the mobile–immobile model (MIM) with time-dependent dispersion coefficient to simulate solute transport through heterogeneous porous media. Observed experimental data of non-reactive solute transport through hydraulically coupled stratified porous media have been simulated using asymptotic and linear time-dependent dispersion functions. Non-Gaussian breakthrough curves comprising long tails are simulated well with the MIM incorporating asymptotic time-dependent dispersion model. The system is under the strong influence of physical nonequilibrium, which is evident by variable mass transfer coefficient estimated at different down-gradient distances. Asymptotic time-dependent functions are capable of capturing the rising limb of the solution phase breakthrough curves with improved accuracy, whereas tailing part simulation capabilities are similar for both asymptotic and linear time-dependent dispersion functions. Further, the temporal moment analysis demonstrated increased spreading, variance for linear dispersion model as compared with asymptotic dispersion model. It is also observed that the first-order mass transfer coefficient varies inversely with travel distance from the input source. It can be concluded from the study that MIM with time-dependent dispersion function is simpler yet sensitive to account for medium’s heterogeneity in a better manner even for small observation distances from the source.