An efficient method and system for the electrochemical treatment of waste water comprising organic and/or inorganic pollutants is disclosed. The system comprises at least first and second solid polymer electrolyte electrolytic cell stacks in which each cell comprises a solid polymer, proton exchange membrane electrolyte operating without catholyte or other supporting electrolyte. The first and second stacks differ either in construction or operating condition. The cell stack design and operating conditions chosen provide for significantly greater operating efficiency.