Benthic microbial fuel cells (BMFC) are devices that remove organic matter (OM) and generate energy from sediments rich in organic nutrients. They are composed of electrodes with adequate different distances and floating air cathodes in an aqueous medium with saturated oxygen. In this study we proposed to design, build, analyze and evaluate a set of BMFCs with floating air cathodes to test the optimal distance between the electrodes, using sediment from the Bay of Campeche as a substrate. For the analysis of OM removal, COD tests, volatile solids (VS), E4/E6 study and FTIR analysis were performed. Power generation was evaluated through polarization curves, cyclic voltammetry and electrochemical impedance spectroscopy (EIS). We achieved a current density and power density at 10 cm depth of 929.7 ± 9.5 mA/m2 and 109.6 ± 7.5 mW/m2respectively, with 54% removal of OM from the sediment, obtaining formation of aliphatic structures. BMFCs are proposed as adequate systems for bioremediation and power generation. The system at 10 cm depth and 100 cm distance between sediment and the floating air cathode had a good performance and therefore the potential for possible scaling.