Evidence shows that flow‐driven unclogging of pore spaces is correlated with permeability variations in fluid‐saturated porous rocks. Due to the well‐established ability of seismic waves to induce transient fluid flow in porous media, permeability changes due to seismically induced unclogging have been proposed to explain hydrogeological phenomena commonly associated with distant earthquakes. In an effort to demonstrate the effects of seismically induced unclogging, laboratory experiments of forced oscillatory flow in centimeter‐scale samples have been performed. However, the corresponding extrapolation of the observations to the field scale has yet to be addressed. In this work, we model the coupling between the strains imposed by propagating seismic body waves and the development of transient flow in porous media following Biot's theory of poroelasticity. To assess the potential of seismically induced unclogging, we use previously reported flow velocity thresholds for which measurable permeability variations were observed. We show that only diffusive waves can induce flow velocities in the order of those capable of initiating unclogging. In heterogeneous media, diffusive waves are created as energy conversion from passing seismic waves at the interfaces separating two porous phases of the medium. We investigate this mesoscale process for body waves propagating across a fault zone as a function of the energy density, frequency, and incidence angle of the waves. Seismically induced unclogging potential in fault zones increases with frequency and imposed strain, although this relation is strongly affected by the incidence angle of the seismic wave, the fault thickness, and the stiffness contrast between the fault and the embedding background.