The investigations show that an undeniable part of future smart energy system, which is to be based on 100% clean energies, is energy storage units. Indeed, due to the intermittent inherent of the main source of renewable energies, e.g., wind and solar, energy storage systems will be highly in service in the future. In this regard, investigation of the impacts of combining nanopowders on the thermal behavior of PCM through a thermal energy storage bed in various operational conditions has been an interesting topic of study in the literature. The current article presents entropy generation assessment of a heat storage unit with a water-based nanoparticle-enhanced PCM under the impact of Lorentz forces. In this system, the nanoparticles are dispersed in the pure phase change material (water) to augment the conductive rate, speeding up the solidification (i.e., the discharging) process. For this, the governing equations are derived with impose of Darcy’s law for the permeable media and homogeneous model for the CuO–water nanomaterial features. The numerical solution method is Galerkin finite element method using FlexPDE software. The results of the simulations are presented for the entropy generation components (including friction, magnetic and thermal effects) and solid fraction contours for various Rayleigh numbers and flow conditions.