In this paper, we discuss laboratory experiments of bentonite swelling and coupled finite element simulations to explicate bentonite extrusion. For the experiments, we developed a swell cell apparatus to understand the bentonite migration to the near-borehole fracture. We constructed the swell cell using acrylic, which comprised of a borehole and open fracture. Initially, the borehole of the swell cell was filled with bentonite and liquid. Then, the apparatus was sealed for observations. Due to the liquid saturation increase of bentonite, its swelling pressure increased. The developed pressure caused the extrusion of bentonite into the fracture, and the flow of bentonite from the borehole decreased with time. Moreover, for the effectiveness of bentonite-based plugging, there is a limiting condition, which represents the relation between the maximum bentonite migration length with the fracture aperture. Additionally, we also performed the bentonite free swelling test to assess the swelling potential to the fluid salinity, and we observed that with the increase of the salinity, the swelling potential decreased. In addition, we present a fully coupled two-phases fluids flow (e.g., liquid and gas) and deformation flow finite element (FE) model for the bentonite column elements and swell cell model. We also combined the Modified Cam Clay (MCC) model and the swelling model for the bentonite deformation flow model. Then, we also present the validation of the bentonite model. To model other sub-domains, we used the poro-elastic model. Additionally, we obtained the transition between the wetting phase (i.e., liquid) and non-wetting phase (i.e., gas) using the Brooks–Corey model. From the finite element results, we observed that due to the liquid intrusion into the bentonite, the developed capillary pressure gradient results in a change of the hydro-mechanical behavior of the bentonite. Initially, we observed that due to the high capillary pressure gradient, the liquid saturation and the swelling pressure increased, which also decreased with time due to a reduction in the capillary pressure gradient. Thereby, the swelling pressure-induced bentonite migration to the fracture also decreased over time, and after the equilibrium state (for a negligible pressure gradient), there was no significant transport of bentonite into the fracture.