Mud pumping in railways occurs when finer particles in the subgrade soils infiltrate through the overlying coarser ballast layer. The finer particle migration can lead to local settlement and cavities in the subgrade soils and consequently causes poor track performance. The micro-scale mechanisms of finer particles infiltrating into a coarser layer are investigated in this study using coupled Computational Fluid Dynamics and Discrete Element Method (CFD-DEM). The early stage of filtration was simulated at the micro-scale with a simplified system where assemblies comprising a base layer of finer particles underlying a filter layer of coarser particles, and an upward seepage flow perpendicular to the interface was employed to trigger base infiltration. Various filter-base size ratios along with different flow conditions were considered to investigate the influence of geometric and hydraulic conditions on infiltration. The simulation results of the fluid behaviours were validated by comparing the numerical, empirical and experimental results of hydraulic conductivity. The hydraulic conductivity of the infiltrated zone was also investigated, which highlighted the capability of CFD-DEM in investigating the hydraulic conductivity change induced by filtration.