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We propose the use of the Lagrangian method Smoothed particle Hydrodynamics (SPH) to model the behaviour of fluids through a pore structure of a volcanic soil core sample. Such studies are of importance to simulate preferential flows which are essential in the leeching of organic and chemical compounds in underground aquifers. Our approach combines X-ray Computed Tomography imaging, and image processing techniques to extract the 3D porous structure of the media studied. Smoothed particle Hydrodynamics modelling simulates water transport in the reconstructed 3D pore network using Navier Stokes governing laws. An isolated pore was considered as a case-based study. We are currently extending our simulation to a full sized pore network.