Clogging is one of the prevalent problems that cause severe damage in the performance, functionality and longevity of granular medium used in geotechnical structures such as filters and stone columns. Despite the growing interest in clogging phenomena, there is a limited number of studies investigating the microscale mechanisms of clogging when fines are flowing into the porous medium under the influence of fluid flow. In this respect, this study aims to employ an advanced numerical approach where the discrete element method (DEM) to model discrete soil particles is combined with computational fluid dynamics (CFD) to model fluid flow governed by Navier–Stokes equations. The numerical results show different patterns of migration and accumulation of fine particles in the given porous media (i.e., stone column) depending on the associated properties of soil and fluid. A set of critical factors that control the clogging potential are also investigated in detail including the influence of hydraulic gradient and characteristics of coarse medium such as its particle sizes. The innovation of this study is the exploration of the micromechanics of clogging, which has not been addressed thoroughly before.