Perfluorinated sulfonated cation-exchange membranes MF-4SC containing 0.5-3.0% of carbon nanotubes (CNTs) have been synthesized. A correlation between the water uptake and transport properties of the membranes in the K +-form and the sensitivity of DP-sensors (with the analytical signal in the form of a Donnan potential) to the analyte and interfering ions in solutions of hydrophobic amino acids (alanine, valine, and phenylalanine) has been found. Hybrid membrane samples that provide the highest sensitivity of DP-sensors to amino acid cations and zwitterions and the lowest sensitivity to hydroxonium ions at pH < 7 in a concentration range of 1.0 × 10-4-1.0 × 10-1 M have been selected. Membrane modification has led to a decrease in the relative error and the relative standard deviation in the determination of amino acid ions by a factor of 3 and 1.5, respectively.