Managed aquifer recharge (MAR) is a strategy within water resources management. However, issues related to clogging have hindered its implementation. The change in permeability of the medium is significantly influenced not only by the macroscopic characteristics of infiltration sand, such as heterogeneity and anisotropy, but also by its microstructural features, including pore structure, morphology and connectivity. Nevertheless, the interactions between fluid flow, particle migration and changes in permeability remain unclear. This study investigates the pore‐scale response mechanisms between fluid flow and pore clogging using a non‐destructive x‐ray computed tomography approach. Our findings indicate that the decrease in permeability due to particle deposition occurs in stages, with particles preferentially accumulating in irregularly shaped pores. The changes in the permeability of the sand column exhibit a negative correlation with alterations in shape factor and tortuosity, while showing a positive correlation with the fractal dimension. As pores become clogged with particles, the increase in tortuosity leads to a longer flow path. Once the sharp edges of the irregular pores are filled with particles, the pore space becomes smoother and more uniform, and the fractal dimension of the pores gradually decreases with further clogging. Based on numerical modelling of particle movement and the clogging process in porous media, it was determined that pressure is greatest in clogged pores. When this pressure reaches a certain threshold, the particles that were previously trapped in the pores are flushed out, leading to uneven changes in normalised hydraulic conductivity and normalised concentration at the outlet. If the pressure is insufficient to dislodge the clogging particles, the water flow path is compelled to change, resulting in a gradual stabilisation of the clogging.