Sediment scouring is a common example of highly dynamic sediment transport. Considering its complexities, the accurate prediction of such a highly dynamic multiphase granular flow system is a challenge for the traditional numerical techniques that rely on a mesh system. The mesh-free particle methods are a newer generation of numerical techniques with an inherent ability to deal with the deformations and fragmentations of a multiphase continuum. This study aims at developing and evaluating a multiphase mesh-free particle model based on the weakly compressible moving particle semi-implicit (WC-MPS) formulation for simulation of sediment scouring. The sediment material is considered as a non-Newtonian viscoplastic fluid, whose behavior is predicted using a regularized μ(I) rheological model in combination with pressure-dependent yield criteria. The model is first validated for a benchmark problem of viscoplastic Poiseuille flow. It is then applied and evaluated for the study of two classical sediment scouring cases. The results show that the high-velocity flow currents and the circulations can create a low-viscosity region on the surface of the sediment continuum. Comparing the numerical results with the experimental measurements shows a good accuracy in prediction of the sediment profile, especially the shape and dimensions of the scour hole.