Water and wastewater treatment accounts for around 4% of energy consumption in the United States. The energy requirements for wastewater and water treatment, as they currently exist, add to the strain on limited fossil fuel resources. Microbial fuel cells (MFCs) can allow direct conversion of the chemical energy in wastewater to electrical energy, increasing the sustainability of wastewater treatment. To allow the implementation of MFCs, more efficient and cost-effective reactor configurations are needed. Also, a better understanding of the microbial communities that facilitate electron transfer in an MFC is required. Several novel MFC designs for water and wastewater treatment are described in this work. Hollow fiber membrane (HFM)-MFCs were developed and a prototype was demonstrated to sustain power production and removal of wastewater organics. An MFC for total nitrogen removal was proposed, and achieved nitrogen removal fluxes comparable to conventional treatment technologies. Additionally, an MFC with a biological cathode was shown to reduce perchlorate, an emerging drinking water contaminant. The role of microorganisms in bioelectrochemical processes was investigated through a variety of studies. First, oxygen crossover from the cathode to the anode was shown to decrease power densities, Coulombic efficiencies, and the abundance of electrode-respiring bacteria. Second, putative electrode-oxidizing bacteria, phylogenetically similar to iron-oxidizing bacteria, were identified in denitrifying and perchlorate-reducing biocathode communities. Finally, despite previous reports to the contrary, similar community structures and MFC performance were observed in MFCs operated at varying external resistances. This research developed novel MFC-based processes for energy-efficient water and wastewater treatment, and contributed to the fundamental understanding of microbial communities within these processes. These results will lead to improved MFC designs and advances the technology toward implementation.