Our challenge in this study was to harvest electricity from organics coexisting in two different phases (water and sediment) in an organics-contaminated benthic environment and to obtain increased current using a multiphase electrode microbial fuel cell (multiphase MFC). The multiphase MFC consisted of a floating electrode (FE), a midelectrode (ME), and a sediment electrode (SE) with no other components. The SE was embedded in sediment; the FE and ME were then overlaid in the water surface layer and in the middle of the water column of an aquarium, respectively. During continuous supply of organics at a COD loading rate of 94 mg of COD L(-1) day(-1) and after the cessation of organics being supplied at COD loading rates of 330 and 188 mg of COD L(-1) day(-1), the multiphase MFC showed the highest current production, as compared to the control MFCs [a floating-type MFC (FT-MFC) and two types of sediment MFCs (SMFC-A and SMFC-B)]. The total charges (in coulombs) of the multiphase MFC integrated from the currents, obtained under the three operating conditions mentioned above, were comparable to the sums of charges for the FT-MFC and SMFC. As a result, this study found that the multiphase MFC can (1) utilize organics in the sediment similarly to SMFCs, (2) use organics in the water phase similarly to FT-MFCs, and (3) obtain increased current analogous to the sum of an SMFC and a FT-MFC. Thus, it is thought that the multiphase MFC developed in this work could be suitable for use in water bodies being continuously or frequently contaminated with organic waste.