Improved techniques are needed to monitor toxic aminophenols in industrial wastewater. Microchip capillary electrophoresis (CE)-electrochemical detection (ECD) can be used to develop miniaturized system providing on-site monitoring. Here, a dual-channel microchip CE-ECD has been applied for the monitoring of aminophenols. The effect of conductance and capacitance between a working electrode and a reference electrode has been studied to minimize the noise that was generated in the amperometric detection. A mixture of aminophenols dissolved in a running buffer has been monitored. A separation efficiency with a plate number of 4770 and a high linear concentration dependence from 100 nM to 1 mM have been achieved for p-aminophenol. As a result, the analysis system has been applied for the monitoring of the pollutants with low detection limits of p-aminophenol (14.6 nM), o-aminophenol (10.6 nM) and m-aminophenol (15.3 nM). Here, we show that a wastewater sample from a natural gas refinery can be monitored using the microchip CE-ECD system.