Selective binding of metal ions to their receptors at the cell membranes is essential for immune reactions, signaling, and opening/closing of the ion channels. Such ligand‐binding‐based pore activities inspire scientists to build metal‐ion‐responsive mesoporous films that can interact with metal ions to tune the ionic nanopore transport. However, to apply these mesoporous films in novel sensing and separation applications, their ligand‐binding‐triggered ionic pore transport needs to be understood fundamentally toward programming the transport of both anions and cations simultaneously and gradually. Herein, it is shown how Ca2+ ion concentration and attachment to the different chemistry silica nanopores tunes finely the nanopore transport of both anions and cations, especially for phosphate‐containing polyelectrolyte (PMEP) functionalized mesopores. This biased ligand binding can gradually regulate the transport of anions and cations, whereas pores without polymers can gradually regulate only the anionic transport. Last, pore polymer functionality related to Ca2+ ion binding also diverts the pores’ adsorption/desorption (reversibility) response. Almost fully reversible Ca2+ binding is observed in non‐functional pores and non‐reversible Ca2+ binding at the PMEP‐modified pores. It is also demonstrated that non/functional pores, even at sub‐µm concentrations, bind only divalent Ca2+ ions, but they are not selective to trivalent Al3+ ions.