I would use the COD (or BOD, depending on the biological accessibility of the matter in the water). The oxygen demand (in g/L or so) gives you the amount of oxygen that would be needed to fully oxidize the wastewater compounds. Oxygen reduction requires two electrons per oxygen atom (4 per O2); you can thus calculate that into an electric charge required for an electrochemical oxidation of the wastewater. You can now measure the actual charge from the MFC and put that into relation to the expeced charge from the delta COD..... 

Does that sound clear?

MFC efficiency

http://2013.igem.org/Team:Bielefeld-Germany/Project/MFC_Efficiency

How do you calculate the coulombic efficiency of a microbial electrolysis cell for biofuel cell

Coulombic efficiency

While generating power is a main goal of MFC operation, we also seek to extract asmuch of the electrons stored in the biomass as possible as current, and to recover as muchenergy as possible from the system. The recovery of electrons is referred to as Coulombicefficiency(Bruce Logan 2008).

The coulombic efficiency (CE) of a cell indicates a measure of electron recovery from the cell. It is also described as the percentage of total charge transferred to the anode surface over the maximum charge extractable upon complete oxidation of the substrate to electricity (Kassongo and Togo, 2010).

Coulombic efficiency is the efficiency with which electrons are transferred in a system tocarry out an electrochemical reaction. This is an important measure of the microbial fuel cellefficiency as it measures the number of coulombs recovered as electrical current. The coulombicefficiency is dependent on two major factors firstly it depends on microorganism carrying out theelectrochemical reaction and secondly the substrate used by the bacteria to generate current (Leeet al., 2008).

Columbic Efficiency (CE) was determined by integrating the current measured over time (t), and compared with the theoretical current on the basis of chemical oxygen demand (COD) removal and calculated as next equation:

Where, 8 is a constant used for COD, based on MO2= 32 gram/mole, 4 electrons exchanged per mole of oxygen, F is the Faraday’s constant (96485 C/mole - electrons), VAn is the volume of medium chamber, and ΔCOD is the change in the Chemical Oxygen Demand (COD) over timet.

Abdullah Ahmad Sir its excellent answer. Please can you refer this article DOI or title. I want to read it. Thanks. Looking for your kind reply