A new nanoparticle-bound polymer stationary phase was prepared by in situ polymerization of methacrylamide (MAA), bis-acrylamide crosslinker, and carboxylated multi-walled carbon nanotubes (multi-walled CNTs; MWNTs), using the abundant double bonds in the cyclopentadienyl rings in MWNT structure, on a silanized capillary. Each intermediate capillary between the synthesis steps was characterized by SEM, by ATR-IR, and by EOF measurements varying the pH, concentration, and volumetric ratios of ACN in running buffers. The resulting EOF profile was comparable to those of two other capillaries with different phase matrices, silica hydride and polybutyl methacrylate (BMA) phases. With the complex functionality of MWNTs on the hydrophilic polyacrylamide network, the MAA-CNT capillary was capable of separating diverse samples with a wide range of polarity and dissociation properties using open-tubular CEC. Besides optimizing CEC conditions, the migration times of samples were analyzed with respect to velocity and retention factors to evaluate electrophoretic and chromatographic contributions to the CEC mechanism. The migration rates of benzoic acids were determined by the electrophoretic mobilities of the various phenolate ions, while phenolic aldehydes and ketones were additionally influenced by chromatographic interactions, such as p-p, electrostatic effects, hydrogen bonding, and hydrophobic interactions. The retention factors were greater for flavonoids, which are polyphenolic, than for simple phenols, but were smaller than those obtained from the hydrophobic BMA-CNT column. A complete well-resolved separation of the cationic forms of tetracyclines was acheived either by electrophoresis or by chromatography in the MAA-CNT capillary, but not in the BMA-CNT and silica hydride-CNT capillaries.