Internal erosion is a major cause of the failure of hydraulic earthen structures. A particular case of such an erosion process is suffusion which constitutes a strongly coupled fluid-solid interaction problem. It is a selective erosion of fine particles from an unstable soil structure leaving behind the granular skeleton which possibly leads to deformations. Such a process may cause modification in the mechanical behaviour of the soil. To study this problem numerically, a model is established based on the discrete element method implemented in Yade software (Smilauer et al. 2015). Periodic boundary conditions are adopted and the soil is represented by a 3D assembly of spherical discrete elements. Such an oversimplified particle’s shape leads to excessive rolling. To overcome this obstacle, rolling resistance was taken into consideration in the inter-particle contact law. Bearing in mind that numerical modelling of suffusion can constitute a difficult task requiring important computational resources due to the direct description of interactions between solid and liquid phases, a one-way coupling with a fluid phase is considered here. However, effects on the soil due to the loss of a fraction of fine particles is investigated either by modelling soils with different grains size distribution and different initial fines content to characterize its influence on the soil microstructure, or by mimicking the suffusion process by defining an extraction criterion of potentially erodible particles. This extraction criterion is based on the size of the particles, constriction sizes, and the velocity of particles under the effect of fluid forces. From these two approaches, we were able to specify the fines content from which their erosion may have a significant influence on the microstructure. Moreover, the defined extraction criterion was able to describe the effect of erosion on the stability of the soil structure.