<p>The Cone penetration test (CPT) is a cornerstone of geotechnical site investigation and a critical tool for assessing soil compaction in agricultural soils, yet the fundamental mechanisms governing the contrasting behavior of dry and saturated soils during penetration remain incompletely understood. This study employs CFD–DEM framework to investigate CPT in granular soils under both conditions. The superior capability of model performance was verified via the Ergun equation test and upward seepage experiments in mono-disperse particle columns Simulations reveal that the mean cone resistance in dry soil is consistently higher than in its saturated soil, a phenomenon attributed to the pore fluid carrying part of the external load and reducing the effective stress transmitted through the particle skeleton. Micromechanical analysis demonstrates that the presence of pore water fundamentally alters the deformation mechanism: in dry soil, deformation is characterized by a wider disturbed zone and larger particle displacements, whereas in saturated soil, viscous damping and pore pressure buildup confine deformation to a more localized region around the cone tip. Furthermore, the evolution of contact fabric shows that dry sand progressively homogenizes towards an isotropic state, while saturated sand exhibits a partial recovery of directional alignment due to fluid-induced stress redistribution. Microhydraulic analysis highlights drag force as the key hydrodynamic mechanism. These insights advance understanding of coupled hydro-mechanical processes during CPT, providing a numerical tool for interpreting field data in variably saturated soils.</p> Graphical Abstract <p></p>