Many analytical techniques have been used to monitor environmental pollutants. But most techniques are not capable to detect pollutants at nanogram levels. Hence, under such conditions, absence of pollutants is often assumed, whereas pollutants are in fact present at low but undetectable concentrations. Detection at low levels may be done by nano-capillary electrophoresis, also named microchip electrophoresis. Here, we review the analysis of pollutants by nano-capillary electrophoresis. We present instrumentations, applications, optimizations and separation mechanisms. We discuss the analysis of metal ions, pesticides, polycyclic aromatic hydrocarbons, explosives, viruses, bacteria and other contaminants. Detectors include ultraviolet–visible, fluorescent, conductivity, atomic absorption spectroscopy, refractive index, atomic fluorescence spectrometry, atomic emission spectroscopy, inductively coupled plasma, inductively coupled plasma–mass spectrometry, mass spectrometry, time-of-flight mass spectrometry and nuclear magnetic resonance. Detection limits ranged from nanogram to picogram levels.