The present work studies the electrochemical oxidation of solutions of hydroquinone (Hy) and p-benzoquinone (Bz). Both compounds are found in the electrochemical oxidation of phenol and they can be considered as a redox couple, so that the main objective is to study the influence of different separators in the global electrochemical reaction of these compounds. Different glass separators as diaphragms, and different ionic exchange membranes (Nafion 350 and 450) have been used as well as one undivided cell, but the results obtained with this last were not very satisfactory. Working with the two different diaphragms, the best behaviour is shown by the glass separator, which has the greatest hydraulic radius. Testing the ionic exchange membranes using Nafion 350, a bigger amount of organic matter is eliminated. The voltage loss due to the separators in the best of the cases represented one 11% of the total potential applied to the electrochemical reactor and the amount of organic matter eliminated is one 25%.