Fundamental understanding of ion transport phenomena in nanopores is crucial for designing the next-generation nanofluidic devices. Due to surface reactions of dissociable functional groups on the nanopore wall, the surface charge density highly depends upon the proton concentration on the nanopore wall, which in turn affects the electrokinetic transport of ions, fluid, and particles within the nanopore. Electrokinetic ion transport in a pH-regulated nanopore, taking into account both multiple ionic species and charge regulation on the nanopore wall, is theoretically investigated for the first time. The model is verified by the experimental data of nanopore conductance available in the literature. The results demonstrate that the spatial distribution of the surface charge density at the nanopore wall and the resulting ion transport phenomena, such as ion concentration polarization (ICP), ion selectivity, and conductance, are significantly affected by the background solution properties, such as the pH and salt concentration.