The increasing production and use of quantum dot (QD) nanoparticles have caused concerns on the possibility of contaminating the aquatic and terrestrial ecosystems with wastes that may contain QDs. Therefore, studies on the behavior of QDs upon interaction with components of the natural environment have become of interest. This study investigated the fluorescence and electrophoretic mobility of carboxylic or amine polyethylene glycol (PEG)-functionalized CdSe/ZnS QDs in the presence of two aquatic humic substances (HS), Suwannee River humic and fulvic acids, using capillary electrophoresis with laser-induced fluorescence detection. Results showed initial enhancement in fluorescence of QDs at the onset of the interaction with HS, followed by fluorescence quenching at longer exposure with HS (>30 min). It was also observed that the electrophoretic mobility of QDs increases with increasing concentration of HS, suggesting an increase in the ratio in charge to hydrodynamic size of the nanoparticles. To determine if the QDs degraded upon interaction with HS, the QD-HS mixtures were dialyzed to separate free Cd2+ from intact QDs, followed by analysis of the solutions using inductively coupled plasma-mass spectrometry. Results suggested that degradation of QDs in the presence of HS did not occur within the period of incubation.