<p>The aquitard, typically composed of clay, plays a crucial role in determining groundwater flow and solute transport behavior in leaky aquifer systems. Electrostatic interactions with clay particles can significantly hinder ion migration, a phenomenon known as the membrane effect. However, existing groundwater solute transport models, which primarily focus on advection–dispersion processes, have limitations in accurately describing solute transport in these systems. To address this issue, this study proposes a solute transport model that incorporates clay membrane effects. The model is based on the advection–dispersion equation and the thermodynamic equation of an unbalanced system. It accounts for both hydraulic and concentration gradients in controlling vertical seepage and integrates membrane effects into diffusion mechanisms. The proposed model was used to simulate vertical salt migration through an aquitard and explore the impact of membrane effects. The results indicate that the clay membrane effects significantly retard vertical seepage and solute transport in the aquitard. Higher chemico-osmotic efficiency coefficients and solute concentrations in the phreatic aquifer result in slower rates of concentration increase over time in the aquitard. The vertical flow velocity in the aquitard, influenced by membrane effects, initially decreases with depth and then increases; over time, this velocity exhibits an initial rapid increase, followed by a decrease, and then another increase. The magnitude of these changes correlates positively with the chemico-osmotic efficiency coefficient and the solute concentration in the phreatic aquifer. Finally, the model’s uncertainties and limitations are extensively discussed, providing a comprehensive evaluation of its reliability.</p>