We report the benefit of using an optimized composite electrode, based on a multiwall carbon nanotubes and epoxy resin, as working electrode in an automated flow system. The optimal composite electrode composition consists in a 10% carbon nanotubes and 90% epoxy resin. This composition provides lower limit of detection and increases the stability and reproducibility of the analytical signal compared to the 20% conventional composition electrodes. Moreover, the standard solutions are on-line prepared with an automated flow system. The integration of the developed carbon nanotube electrodes in the proposed flow system provides a highly sensitive analyzer for free chlorine determination in water down to the 20microgL(-1). The working range was found to be 0.02-4mgL(-1) with an analysis time of 60s. The system sensitivity was maintained into the control limits (+/-2sigma) for one month, with a mean value of -0.146 (+/-0.008) microALmg(-1). Validation of the analytical system has been performed by the successful determination of free chlorine in tap water and swimming pools water samples.