Due to the difficult access of the electrolyte into the nanoconfined space of nanoporous reduced graphene oxide (rGO) electrodes, achieving the optimal electrochemical performance of these devices becomes a challenge. In this work, the dynamics of interfacial-governed phenomena are investigated during a voltage-controlled electrochemical activation of nanoporous rGO electrodes that leads to an enhanced electrochemical performance in terms of areal capacitance and electrochemical impedance. In situ/operando characterization techniques are used to reveal the dynamics of the irreversible material changes introduced during the activation process, including ionic diffusion and water confinement within the nanopores, along with the reduction of oxygenated groups and the decrease of the rGO interlayer distance. Furthermore, operando techniques are used to uncover the origin of the complex polarization-dependent dynamic response of rGO electrodes. The study reveals that the reversible protonation/deprotonation of remaining functional groups and the cation electro-adsorption/desorption process in the graphene basal plane govern the pseudocapacitive performance of nanoporous rGO electrodes. This work brings new understanding of the complex interplay between surface chemistry, ion confinement, and desolvation processes occurring during electrochemical cycling in nanoporous rGO electrodes, offering new insights for designing high-performing electrodes based on nanoporous rGO.