The seismoelectric method is based on the capacity of seismic waves to generate measurable modifications of the electrical field in porous media. Even though it combines the advantages of seismic and geoelectrical methods, it remains largely underused in hydrogeophysics. Its signal results from an electrokinetic coupling that can be modeled using either the coupling coefficient or the effective excess charge density. The traditional approach is based on the frequency-dependent coupling coefficient, which relates the pressure drop with the change in the electrical potential. A more recent approach consists of describing the excess charge that is effectively dragged by water flowing within the pores. We have developed a new model for the frequency-dependent effective excess charge density. For this, we make use of a mechanistic upscaling of the electrokinetic coupling in a capillary. This novel approach introduces inertial effects arising within the pore space in the flux-averaging procedure to explain the frequency dependence of the effective excess charge density. The presented model is successfully compared to previous models and published data. This new frequency-dependent upscaling approach has the potential of fundamentally improving our current understanding of the seismoelectrical signal in more complex environments, such as partially saturated and fractured media.