Dye-functionalized mesoporous silica has gained considerable attention for use in optical applications. Much interest into the tunable functionality of these small-scale optical materials has been the focus for possible use in lasers, light filters, sensors, solar cells, and photocatalysis. Extensive exploration into functionalizing mesoporous silica has been made using sol-gel methods for incorporating polymeric dyes within the pore channels of the silica network to modify optical properties. However, research so far has been focused on functionalization of mesoporous silica powders or films on dense substrates, limiting applications in practice because of the difficult accessibility of mesopores. In this paper, we studied the development of hierarchically-structured mesoporous silica with chromophore dye molecules covalently linked within the channel walls of pores for the selective adsorption and detection of specific ions and chemical compounds. Hierarchically-structured, unidirectionally-aligned mesoporous silica was synthesized within the pores of polycarbonate membranes by surfactant-assisted sol electrophoretic deposition. After the removal of surfactants from the mesopores, the inner surface of the mesopores was functionalized with silane-containing chromophore molecules through self-assembly. Full coverage of these dye molecules on the surface of the mesopores was anticipated due to the fact that these reactant chromophore molecules, in solution, migrate through the pores. The organic chromophore dye molecules, assembled onto the surface of the mesopores, would have the amino groups exposed to the surface. These groups would have the capability to selectively interact with ions or chemical compounds in solution, for instance lead ions in water. Hence, the absorption spectrum of the chromophore dye molecules attached to the mesopores of silica was altered after exposure to lead ions in solution. In addition, the ion concentration in solution also differed. Such functionalized, hierarchically-structured mesoporous silica would have applications such as membranes for removal of, and sensors for, detecting trace amounts of ions and chemical compounds in water and air.