Increases in permeability of natural reservoirs and aquifers by passing seismic waves have been well documented. If the physical causes of this phenomenon can be understood, technological applications would be possible for controlling the flow in hydrologic systems or enhancing production from oil reservoirs. The explanation of the dynamically increased mobility of underground fluids must lie at the pore level. The natural fluids can be viewed as two-phase systems, composed of water as the wetting phase and of dispersed non-wetting globules of gas or organic fluids, flowing through tortuous constricted channels. Capillary forces prevent free motion of the suspended non-wetting droplets, which tend to become immobilized in capillary constrictions. The capillary entrapment significantly reduces macroscopic permeability. In a controlled experiment with a constricted capillary channel, we immobilize the suspended ganglia and test the model of capillary entrapment: it agrees precisely with the experiment. We then demonstrate by direct optical pore-level observation that the vibrations applied to the wall of the channel liberate the trapped ganglia if a predictable critical acceleration is reached. When the droplet begins to progressively advance, the permeability is restored. The mobilizing acceleration in the elastic wave, needed to “unplug” an immobile flow, is theoretically calculated within a factor of 1–5 of the experimental value. Overcoming the capillary entrapment in porous channels is hypothesized to be one of the principal pore-scale mechanisms by which natural permeabilities are enhanced by the passage of elastic waves.