Investigating the flow behavior in microfluidic systems has become of interest due to the need for precise control of the mass and momentum transport in microfluidic devices. In multilayered-flows, precise control of the flow behavior requires a more thorough understanding as it depends on multiple parameters. The following paper proposes a microfluidic system consisting of an aqueous solution between a moving plate and a stationary wall, where the moving plate mimics a charged oil–water interface. Analytical expressions are derived by solving the nonlinear Poisson–Boltzmann equation along with the simplified Navier–Stokes equation to describe the electrokinetic effects on the shear-driven flow of the aqueous electrolyte solution. The Debye–Huckel approximation is not employed in the derivation extending its compatibility to high interfacial zeta potential. Additionally, a numerical model is developed to predict the streaming potential flow created due to the shear-driven motion of the charged upper wall along with its associated electric double layer effect. The model utilizes the extended Nernst–Planck equations instead of the linearized Poisson–Boltzmann equation to accurately predict the axial variation in ion concentration along the microchannel. Results show that the interfacial zeta potential of the moving interface greatly impacts the velocity profile of the flow and can reverse its overall direction. The numerical results are validated by the analytical expressions, where both models predicted that flow could reverse its overall direction when the interfacial zeta potential of the oil–water is above a certain threshold value. Finally, this paper describes the electroviscous effect as well as the transient development of electrokinetic effects within the microchannel.