The potential of electrokinetic remediation technologies (EKR) for the removal of different contaminants from subsurface porous media has been increasingly recognized. Despite electrokinetic applications have shown promising results, quantitative understanding of such systems is still challenging due to the complex interplay between physical transport processes, electrostatic interactions, and geochemical reactions. In this study, we perform a model-based analysis of electrokinetic transport in saturated porous media. We investigate the effects of: (i) Coulombic interactions between ions in the system mobilized by electromigration, (ii) reaction kinetics on the overall removal efficiency of a non-charged organic contaminant, and (iii) dimensionality and different electrode configurations. The results show that such effects play a major role on the performance of electrokinetic systems. The simulations illuminate the importance of microscopic processes, such as electrostatic interactions and ion-specific diffusivities, and their non-intuitive macroscopic impact on the delivery of charged amendments and on the efficiency of contaminant removal. The insights of this study are valuable to improve and optimize the design and the operational strategies of electrokinetic remediation systems.