Particle bridging owing to the confinement of the pore structure affects the transport and retention of particles in porous media. Particle motion driven by gravities were well investigated, whose filtration is mainly affected by the ratio of the particle diameter to the pore throat size of the medium. However, particles whose motions are driven by the fluid is essential to be investigated for particle separation from the carrying fluid. In this study, the motion of particles was driven by the liquid when passing through a water-saturated porous medium. The fluid–particle flow in a porous medium was modeled using computational fluid dynamics–discrete element method. The motion of particles in the slurry was traced in the porous medium, which enabled particle clogging to be directly precited by the interaction between the particles and pore surfaces by assessing the exact location of each particle. The pressure and flow field of the liquid were investigated, and the variation in flow path owing to particle clogging was predicted. The hydrodynamic study also showed that the Stokes number and particle concentration determined the particle clogging at the pore throats of the porous medium. Increasing the fluid velocity of particles such that the Stokes number was almost equal to 1 increased the separation efficiency of particles. Further increasing the fluid velocity reduced the residence time, which reduced the separation efficiency of the particles.