Triggering the interaction of nanomaterials with molecules by means of electrical potentials in aqueous media remains challenging, especially if 3D through-flow systems are used as electrodes, as in potential-controlled liquid chromatography (PCC). In this paper, multi-walled carbon nanotubes (MWCNTs) function as a particulate packed bed electrode in order to study the system’s response to various applied potentials and electrolyte compositions. The process principle was analyzed using chronoamperometry and cyclic voltammetry. Applying an electrical potential to the hydrophilic MWCNTs induces the presence of both capacitive and faradaic currents. This leads, over time, to a degradation of the electrode due to structural changes of the MWCNT matrix and an increase in redox reactions on the surface. The role of the electrochemical double layer (EDL) is highlighted as a main player in the process, directly influencing the adsorption capability of the electrode. The EDL rearrangement time and coverage radius depend on the composition of the mobile phase and on the potential applied. The capacity of the electrode for the target (maleic acid) increases at high positive potentials (+800 mV vs. Ag/AgCl), while the presence of electrolytes leads to a capacity decrease. Our research enhances the understanding of capacitive through-flow cells.