We prepared colloidal crystals by self-assembly of gold-coated silica nanospheres, and free-standing nanoporous membranes by sintering these colloidal crystals. We modified the nanopore surface with ionizable functional groups, by forming a monolayer of L-cysteine or by surface-initiated polymerization of methacrylic acid. Diffusion experiments for the cationic dye Rhodamine B through L-c-ysteine-modified membranes showed a decrease in flux upon addition of an acid due to the nanopore surface becoming positively charged. Diffusion experiments for the neutral dye, ferrocene-carboxaldehyde, through the PMAA-modified membranes showed a 13-fold increase in flux upon addition of an acid resulting from the protonated polymer collapsing onto the nanopore surface leading to larger pore size. Our results demonstrate that SiO2@Au core shell nanospheres can self-assemble into colloidal crystals and that transport through the corresponding surface-modified Au-coated colloidal membranes can be controlled by pH.