In this work, we have studied the pH-dependent surface charge nature of nanoporous graphene. This has been investigated by membrane potential and by streaming current measurements, both with varying pH. We observed a lowering of the membrane potential with decreasing pH for a fixed concentration gradient of potassium chloride (KCl) in the Donnan dominated regime. Interestingly, the potential reverses its sign close to pH 4. The fitted value of effective fixed ion concentration (C̅R) in the membrane also follows the same trend. The streaming current measurements show a similar trend with sign reversal around pH 4.2. The zeta potential data from the streaming current measurement is further analyzed using a 1-pK model. The model is used to determine a representative pK (acid–base equilibrium constant) of 4.2 for the surface of these perforated graphene membranes. In addition, we have also theoretically investigated the effect of the PET support in our membrane potential measurement using numerical simulations. Our results indicate that the concentration drop inside the PET support can be a major contributor (up to 85%) for a significant deviation of the membrane potential from the ideal Nernst potential.