The frequent use of earth materials for hydraulic capping and waste containment requires improved understanding of relationships between soil mechanical dynamics and its hydraulic and transport properties. We study deformation of pores embedded in viscoplastic soils subjected to anisotropic remote stress using Finite Element analysis (FEA). FEA enables consideration of complex pore geometries, and provides a detailed picture of pore cross-section change and subsequent change in hydraulic conductivity. Images of deforming aggregate beds monitored using X-ray computer assisted tomography (CAT) coupled with independently measured soil rheological properties were used to test the FEA model. Pore deformation for different remote stresses was compared with data from compaction experiments using modeling clay and soil aggregates. The impact of inter-aggregate pore deformation on hydraulic conductivity was obtained from detailed FEA model and compared with standard approximations (e.g., using the hydraulic radius). The evolution of complex pore shapes during compaction on prediction of saturated hydraulic conductivity will be discussed.