Surface charge plays a very important role in biological processes including ionic and molecular transport across a cell membrane. Placement of charges and charge patterns on walls of polymer and solid-state nanopores allowed preparation of ion-selective systems as well as ionic diodes and transistors to be applied in building biological sensors and ionic circuits. In this article, we show that the surface charge of a 10 nm diameter silicon nitride nanopore placed in contact with a salt gradient is not a constant value, but rather it depends on applied voltage and magnitude of the salt gradient. We found that even when a nanopore was in contact with solutions of pH equivalent to the isoelectric point of the pore surface, the pore walls became charged with voltage-dependent charge density. Implications of the charge gating for detection of proteins passing through a nanopore were considered, as well. Experiments performed with single 30 nm long silicon nitride nanopores were described by continuum modeling, which took into account the surface reactions on the nanopore walls and local modulation of the solution pH in the pore and at the pore entrances. The results revealed that manipulation of surface charge can occur without changing pH of the background electrolyte, which is especially important for applications where maintaining pH at a constant and physiological level is necessary. The system presented also offers a possibility to modulate polarity and magnitude of surface charges in a two-electrode setup, which previously was accomplished in more complex multielectrode systems.