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Electrostatic potential profiles are vital for understanding and controlling electroosmosis as well as particle mixing. The shape and magnitude of this profile—particularly a key parameter called the zeta potential (ζ)—directly dictate the speed and direction of fluid flow when an electric field is applied. The role of temperature in modifying this important parameter has not been analyzed from a mathematical approach, and it is relevant for improving the design of microfluidic devices and technologies involving capillary electrophoresis for non-isothermal systems. In this study, two electrophoretic cell geometries are investigated under non-isothermal conditions. A heat-transport model (with heat generation and Dirichlet boundary conditions) is coupled into the Poisson–Boltzmann equation to obtain zeta potential profiles for different temperature distributions. In addition, the Navier–Stokes equation for the electroosmotic case is solved to obtain velocity profiles, including examples of flow reversal under temperature development. Numerical analysis for rectangular and cylindrical geometries indicates that large temperature gradients produce significant zeta-potential changes and can induce multiple flow reversals; effects are more pronounced at high Joule-heating values, while small temperature differences yield approximately linear electrostatic potential behavior and typical laminar profiles.