Ionic flux through a composite membrane structure, containing vertically aligned carbon nanotubes crossing a polystyrene matrix film, was studied as a function of chemical end groups at the entrance to carbon nanotubes' (CNTs) cores. Plasma oxidation during the membrane fabrication process introduced carboxylic acid groups on the CNTs' tips that were modified using carbodiimide mediated coupling between the carboxylic acid and an accessible amine groups of the functional molecule. Functionalization molecules included straight chain alkanes, anionically charged dye molecules, and an aliphatic amine elongated by polypeptide spacers. Functionalization was confirmed by FTIR spectroscopy, and areal functional density was estimated by transmission electron microscopy studies of thiol terminated sites decorated by nanocrystalline gold. The transport through the membrane of two different sized but equally charged molecules (ruthenium bipyridine [Ru-(bipy)(3)(2+)] and methyl viologen [MV2+]) was quantified in a U-tube permeation cell by UV-vis spectroscopy. Relative selectivity of the permeates varied from 1.7 to 3.6 as a function of tip-functionalization chemistry. Anionic charged functional groups sharply increased the flux of the cationic permeates. This effect was reduced at higher solution ionic strength consistent with shorter Debye screening length. The observed selectivities were consistent with a hindered diffusion model with functionalization at the CNT tip and not along the length of the CNT core.