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Abstract The susceptibility of a granular soil to suffusion is strongly dependent on its grain size distribution (GSD) and the mechanical and hydraulic conditions it is subjected to. This study investigates the onset of suffusion considering the effect of confining pressure and stress anisotropy using a fully resolved computational fluid dynamics and discrete element method (CFD–DEM). Three benchmarks, including the sedimentations of single and two adjacent spheres and the classic one‐dimensional (1D) consolidation are performed to demonstrate the capability of this method for high‐fidelity particle‐fluid simulations. A modified hydraulic criterion for the onset of suffusion considering stress anisotropy is presented. The microstructural changes of soil specimens before and during global suffusion are inspected, with emphasis on the evolutions of particle kinetic energy and displacements, force chain networks, and stress anisotropy. We found that the critical hydraulic gradient is negatively correlated with the confining pressure and the degree of stress anisotropy. Fine particles in the soil matrix are locally detached at small hydraulic gradients before the apparent global suffusion, as manifested by the variation of particle kinetic energy and coordination numbers. The roles of different contact types on force transmission and stress anisotropy in eroded specimens are also examined.