Sediment microbial fuel cell (SMFC) is a special type of microbial fuel cells that can be deployed in a natural water body for energy production and contaminant removal. This MS project aims to explore whether it will be viable to apply SMFCs for wastewater treatment. Experimental SMFCs were studied in several configurations and operational modes for organic removal, nitrate reduction, and energy recovery. When treating an artificial secondary effluent for nitrate removal, the SMFC could remove 44% of the nitrate, higher than that without electricity generation. The enhanced removal was attributed to the supply of electrons to nitrate reduction in the aqueous phase through oxidizing the organics in the sediment. The lack of a proper separator between the anode and the cathode led to the failure of the SMFC when treating an artificial raw wastewater. Ion exchange membranes were incorporated into the MFCs that were installed in a lab-scale open water pond (150 L in volume). Such a system achieved 100% COD removal and more than 75% removal of ammonium nitrogen. However, denitrification remained as a challenge because of a lack of anoxic zone. To reduce the cost of the cathode catalysts, a polymer-based carbon cloth was investigated and exhibited better performance than bare carbon cloth. The results of this MS project have demonstrated that SMFCs in the absence of a proper separator cannot be applied for wastewater treatment. A membrane-based MFC system integrated with open pond may function as a wastewater treatment system, though nitrogen removal efficiency must be improved.