A new multi-compartment microfluidic device was developed to simultaneously desalinate and recover valuable metal ions from aqueous streams mimicking metal plating and mining tailing wastewaters. Heavy and valuable metal ions including copper, zinc, nickel, silver and zinc/copper ionic mixtures were selectively transferred from the feed solution to a reduction chamber through ion-exchange membranes under the influence of an electrical field. A porous and conductive carbon cloth material was used as reduction platform, which led to improved desalination efficiencies, previously unachievable due to inevitable poisoning and degradation of the membranes at high current densities. The use of conductive carbon clothes enabled the recovery of the metal deposits, post reduction, through a simple electro-oxidation process. This novel microfluidic method, using ion-exchange materials as channel walls, has also the potential for the controlled decoration of materials with metal nano particle patterns and for the regeneration of rare earth trace contaminants by electro-sorption assisted electrodialysis.