While the frequency-dependence of permeability under fully saturated conditions has been studied for decades, the corresponding characteristics of partially saturated porous media remain unexplored. Notably, it is not clear whether the use of effective pore fluid approaches under such conditions is valid. To address this issue, we propose a method that allows us to obtain dynamic permeability functions for partially saturated porous media. To this end, we conceptualize the considered pore space as a bundle of capillary tubes of different radii saturated by two immiscible fluid phases. We then solve the Navier–Stokes equations within the pore space and define a capillary pressure–saturation relationship, which permits to obtain saturation- and frequency-dependent effective permeability estimates. The application of this method to a realistic model of an unconsolidated granular sediment demonstrates that dynamic effective permeability functions for wetting and non-wetting fluid phases exhibit distinct characteristics, thus rendering effective pore fluid approaches inadequate. Finally, we explore the capability of the seminal dynamic permeability model developed by Johnson et al. [J. Fluid Mech. 176, 379 (1987)] to account for the effects of partial saturation. We find that the frequency scaling proposed by Johnson et al. prevails in partially saturated scenarios. However, the parameters associated with this model need to be redefined to account for saturation-dependent effects.