Self-assembled silica colloidal crystals (opals) have been surface-modified with organic moieties capable of carrying positive or negative charges, capable of forming non-covalent complexes via hydrogen bonding and pi-pi stacking, and with polymers. The transport of ions and molecules through these nanoporous materials have been studied using cyclic voltammetry and spectrophotometrc techniques. Factors including surface charge, nanopore size and non-covalent interactions have been shown to control the transport. These factors and transport mechanisms will be discussed.