Microbial fuel cell (MFC)-based technologies are promising technologies for direct energy production from various wastewaters and waste streams. Beside electrical power production, more emphasis is recently devoted to alternative applications such as hydrogen production, bioremediation, seawater desalination, and biosensors. Although the technologies are promising, a numerous of hurdles need to be overcome before that field applications are economically feasible. The main purpose of this work was to improve the performance, reduce the construction cost, and expand the application scopes of MFC-based bio-electrochemical systems. To reduce the energy cost in nitrogen removal and during the same process achieve phosphorus elimination, a sediment-type photomicrobial fuel cell was developed based on the cooperation between microalgae (Chlorella vulgaris) and electrochemically active bacteria. The main removal mechanism of nitrogen and phosphorus was algae biomass uptake, while nitrification and denitrification process contributed to part of nitrogen removal. The key factors such as algae concentration, COD/N ratios and photoperiod were systemically studied. A self-powered submersible microbial electrolysis cell was developed for in situ biohydrogen production from anaerobic reactors. The hydrogen production increased along with acetate and buffer concentration. The hydrogen production rate of 32.2 mL/L/d and yield of 1.43 mol-H2/mol-acetate were achieved. Alternate exchanging the function between the two cell units was found to be an effective approach to inhibit methanogens. A sensor, based on a submersible microbial fuel cell, was developed for in situ monitoring of microbial activity and biochemical oxygen demand in groundwater. Presence or absence of a biofilm on the anode was a decisive factor for the applicability of the sensor. Temperature, pH, conductivity and inorganic solid content were significantly affecting the sensitivity of the sensor. The sensor showed good performance both with artificial and real groundwater. A submersible microbial fuel cell sensor was developed for in situ and real time monitoring of dissolved oxygen (DO) in environmental waters. The current density produced by the sensor increased linearly with DO level up to 8.8±0.3 mg/L. The sensor ability was further explored under different environmental conditions. The sensor can measure DO in different environmental waters with less deviations. To improve the voltage output of MFC from lake sediment, an innovative self-stacked submersible MFC was developed. The system successfully produced a maximum power density of 294 mW/m2 and had an open circuit voltage (OCV) of 1.12 V. In addition, voltage reversal was studied in detail in terms of its cause, determining parameters and elimination method. The internal resistance and OCV were the most important parameters for predicting voltage reversal. Use of a capacitor was found to be an effective way to prevent voltage reversal and at the same time store power. A sediment-type MFC based on two pieces of bioelectrodes was employed as a novel in situ applicable approach for nitrate/nitrite removal, as well as electricity production from eutrophic lakes. The nitrogen removal and power generation were limited by the DO level in the water and acetate level injected to the sediment. The proposed approach may broad the application of sediment MFC technology. A novel submersible microbial desalination cell was developed as an in situ and non-invasive approach for nitrate removal from groundwater. The system performance in terms of power generation and nitrate removal efficiency were investigated. The effects of hydraulic retention time, external resistance, other ionic species in the groundwater and external nitrification on the system performance were also elucidated. Over 90% of nitrate was removed from groundwater without energy input, water pressure, draw solution, additional electron donor or risk of bacteria discharge. Such a new system may offer a promising avenue for drinking water treatment and energy recovery.