We report the development of an MCM-41 mesoporous support that is functionalised with saccharides at the pore outlets and contains the dye [Ru(bipy)3]2+ in the pores (solid S1; bipy=2,2′-bipyridyl). For this hybrid system, the inhibition of mass transport of the dye from the pore voids to the bulk solution in the presence of borate is demonstrated in water at neutral pH. The formation of the corresponding boroester derivative is related to the selective reaction of borate with the appended saccharides. This control is selective and only anion borate, among several anions and cations, can act as a molecular tap and inhibit the delivery of the entrapped guest. Additionally, the S1–borate system behaves as pH-controlled gatelike scaffolding. This pH-responsive release can be achieved in an acidic pH (due to hydrolysis of the boroester), whereas the system remains closed at neutral pH. Molecular dynamic simulations using force-field methods have been made to theoretically study the open/close borate-driven mechanism. A mesoporous silica structure was constructed for this purpose, taking the plane (1−11) of the β-cristobalite structure as a base on which hexagonal nanopores and anchored saccharide derivatives were included. The final model shows a highly flexible nanopore diameter of approximately 12.5 Å of similar size to the [Ru(bipy)3]2+ complex (ca. 12 Å). However, the anchoring of borate to the appended saccharides results in a remarkable reduction of the pore size (down to ca. 6.4 Å) and a significant constraint in the flexibility and mobility of the saccharides. The theoretical calculations are in agreement with the experimental results and enable visualisation of the functional borate-driven dye-delivery-inhibition outcome.