The evolution of granular beds subjected to upward seepage flow is investigated using a coupled DEM-fluid model implemented by Catalano et al. in the open-source software Yade-DEM. Firstly, filtration properties of a coarse narrowly graded material are analyzed by simulating the transport of smaller particles from a base layer through the coarse filter by gravitational loading or downward flow with uniform pressure gradient. The results are analysed on the basis of the constriction size distribution (CSD) of the filter which describes statistically the sizes of throats between pores in the material. Secondly, we examine the results obtained when, instead of two different layers, the coarse and fine materials are initially mixed in one unique layer and subjected to gravity. Thirdly, this mixture of coarse and fine particles is subjected to both gravity and a non-uniform pressure gradient, by injecting the fluid in one point below the layer, as inspired by previous experiments. Similar channeling patterns are obtained in both experiments and simulations when the boundary condition at the injection point is an imposed flux. This boundary condition results in a recirculation mechanism that remains confined in a finite zone around the injection point as long as the flux is below a threshold value. By simulating an imposed pressure condition, we finally show that instabilities can be triggered by the transport of small particles away from the injection point. This segregation process results in a lower porosity and an increased pressure gradient above the eroded zone, so that the instability-triggering pressure gradient in bi-dispersed mixtures is lower than in mono-dispersed mixtures