The electrogenerated mediator oxidation process is capable of oxidizing organic compounds to the final step, producing CO2. It requires the use of separate compartments for the anode and cathode. A considerable electric charge is necessary to decompose long carbon chains and high-intensity electrochemical reactors are needed for use at industrial scale. A variety of porous and microporous ceramic separators (frits) have been used in industrial-scale electrochemical cells, for example, hollow cylinders made of various porous ceramics have been used to build annular cells. However, these separators exhibit a high electric resistance and one alternative is to use a perfluorosulfonic ion-exchange membrane. It is, therefore, essential to determine the flows through this membrane in order to optimize process operation. The authors describe the ion and water flows through the membrane, and their influence on the process.