Noncovalent approaches to achieve smart ion-transport regulation in artificial nanochannels have garnered significant interest in the recent years because of their advantages over conventional covalent routes. Herein, we demonstrate a simple and generic approach to control the surface charge in mesoporous silica nanochannels by employing π-electron-rich charged motifs (pyranine-based donors) to interact with the surface of mesoporous silica modified with π-electron-deficient motifs (viologen-based acceptors) through a range of noncovalent forces, namely, charge-transfer, electrostatic, and hydrophobic interactions. The extent of each of these interactions was independently controlled by molecular design and pH, while employing them in a synergistic or antagonistic fashion to modulate the binding affinity of the charged motifs. This enabled the precise control of the surface charge of the nanochannels to achieve multiple ion-transport states. © 2018 American Chemical Society.