Pulsed electric field (PEF) modes of electrodialysis (ED) are known for their efficiency in mitigating the fouling of ion-exchange membranes. Many authors have also reported the possibility of increasing the mass transfer/desalination rate and reducing energy costs. In the literature, such possibilities were theoretically studied using 1D modeling, which, however, did not consider the effect of electroconvection. In this paper, the analysis of the ED desalination characteristics of PEF modes is carried out based on a 2D mathematical model including the Nernst–Planck–Poisson and Navier–Stokes equations. Three PEF modes are considered: galvanodynamic (pulses of constant electric current alternate with zero current pauses), potentiodynamic (pulses of constant voltage alternate with zero voltage pauses), and mixed galvanopotentiodynamic (pulses of constant voltage alternate with zero current pauses) modes. It is found that at overlimiting currents, in accordance with previous papers, in the range of relatively low frequencies, the mass transfer rate increases and the energy consumption decreases with increasing frequency. However, in the range of high frequencies, the tendency changes to the opposite. Thus, the best characteristics are obtained at a frequency close to 1 Hz. At higher frequencies, the pulse duration is too short, and electroconvective vortices, enhancing mass transfer, do not have time to develop.