During the last years, several authors have focused on the characterization of the size and charge of the nanoparticles by capillary electrophoresis. However, considering that nanoparticles are generally suspended in a solvent different from those commonly used as background electrolytes (BGE), an appropriate characterization of the behavior of the nanoparticles in the sample-BGE interface is required, as this might affect the overall electrophoretic behavior of the nanoparticles. In the present work, we address the evaluation of the behavior of COOH-coated maghemite nanoparticles in the vicinity of a pH boundary. To do so, different suspensions of nanoparticles prepared in acid media were injected into a borate/NaOH pH 9.5 BGE. The formation and evolution of boundaries in the sample-BGE interface in such systems was modeled by computer simulation. A systematic evaluation of the effect that parameters such as the co-ion, the sample pH or the injection time have on the electrophoretic behavior of the nanoparticles was carried out.