Water soluble positively charged 2-(dimethylamino)ethanethiol (DAET)-protected core-shell CdSe/ZnS quantum dots (QDs) were synthesized and incorporated within negatively charged Nafion polymer films. The water soluble QDs were characterized using UV-visible and fluorescence spectroscopies. Nafion/QDs composite films were deposited on glassy carbon electrodes and characterized using cyclic voltammetry. The electrochemiluminescence (ECL) using hydrogen peroxide as co-reactant was enhanced for Nafion/QDs composite films compared to films of the bare QDs. Significantly, no ECL was observed for Nafion/QDs composite films when peroxydisulfate was used as the co-reactant, suggesting that the permselective properties of the Nafion effectively exclude the co-reactant. The ECL quenching by glutathione depends linearly on its concentration when hydrogen peroxide is used as the co-reactant, opening up the possibility to use Nafion/QDs composite films for various electroanalytical applications.