Abstract: A microbial electrochemical cell is described herein. The cell includes an anode electrode disposed in an anoxic environment below a water surface. The anode receives electrons from anaerobic decomposition of organic matter or other reduced compounds by microbes in sediment below the water surface. The cell also includes a cathode electrode disposed in an environment at a higher electrochemical potential than the anoxic environment. The cathode is electrically connected to the anode to receive the electrons from the anode. A reference electrode is disposed in the environment at the higher electrochemical potential than the anoxic environment. A potentiostat is electrically connected to each of the anode, the cathode and the reference electrode and is configured to receive electrons from the anode and control distribution of the electrons to the cathode based on a potential difference between the anode and the reference electrode. Methods of remediating aquaculture sediment are also described.