Online monitoring of groundwater quality in shallow wells to detect faecal or organic pollution could dramatically improve understanding of health risks in unplanned peri-urban settlements. Microbial fuel cells (MFC) are devices able to generate electricity from the organic matter content in faecal pollution making them suitable as biosensors. In this work, we evaluate the suitability of four microbial fuel cell systems placed in different regions of a groundwater well for the low-cost monitoring of a faecal pollution event. Concepts created include the use of a sediment/bulk liquid MFC (SED/BL), a sediment/sediment MFC (SED/SED), a bulk liquid/air MFC (BL/Air), and a bulk liquid/bulk liquid MFC (BL/BL). MFC electrodes assembly aimed to use inexpensive, durable, materials, which would produce a signal after a contamination event without external energy or chemical inputs. All MFC configurations were responsive to a contamination event, however SED/SED and BL/Air MFC concepts failed to deliver a reproducible output within the tested period of time. BL/BL MFC and SED/BL MFCs presented an increase in the average current after contamination from −0.75 ± 0.35 μA to −0.66 ± 0.41 μA, and 0.07 ± 0.2 mA to 0.11 ± 0.03 mA, respectively. Currents produced by the SED/BL MFC (SMFC) were considerably higher than for the BL/BL MFCs, making them more responsive, readable and graphically visible. A factorial design of experiments (DOE) was applied to evaluate which environmental and design factors had the greatest effect on current response in a contamination event. Within the ranges of variables tested, salinity, temperature and external resistance, only temperature presented a statistically significant effect (p = 0.045). This showed that the biosensor response would be sensitive to fluctuations in temperature but not to changes in salinity, or external resistances produced from placing electrodes at different distances within a groundwater well.