<p>In this study, we employ the Boltzmann dynamics approach to investigate nanofiltration phenomena in electrodialysis systems, with a particular focus on the temporal evolution of permeate flux. By solving the Boltzmann equation, which accounts for the statistical behavior of particles, we simulate ion and water molecule transport through membranes while capturing crucial non-equilibrium effects. Unlike conventional mean-field models, this approach explicitly incorporates particle velocity distributions and interactions, offering a more detailed understanding of transport mechanisms. Our findings reveal that permeate flux is significantly influenced by membrane resistance, feed concentration, applied voltage, viscosity, permeability, and transmembrane pressure. The results show a time-dependent decline in permeability due to pore clogging and structural changes, as well as an interplay between ion transport mechanisms and electro-osmotic drag. A comparative analysis with existing theoretical models, such as the Nernst–Planck equation coupled with the Poisson equation, highlights the advantages of Boltzmann dynamics in describing fluctuations, correlations, and concentration polarization effects. Furthermore, our analysis demonstrates that low-viscosity fluids enhance fluid–membrane interactions, accelerating clogging processes, while higher resistance results in a faster decline in permeate flux. Additionally, the application of an electric field can enhance permeate transport initially but may also contribute to long-term structural modifications of the membrane. These insights contribute to the optimization of membrane design and operational conditions for improved filtration efficiency.</p>