Microorganisms can remove selenate (SeO4-2) in water by converting it to elemental selenium nanoparticles. Conventional biological reactors usually simultaneously produce intracellular and extracellular elemental selenium nanoparticles or only produce intracellular selenium nanoparticles. Recovery of the intracellular selenium nanoparticles is commercially prohibitive due to high energy demand for separating the intracellular selenium from the biomass components. This work addressed the challenge for the first time by using a biocathode-based bioelectrochemical reactor that produced extracellular selenium nanoparticles only, which eliminated the need for separating the intracellular selenium from the biomass. The continuous-flow bioelectrochemical reactor removed > 99.6% of the selenate at a selenate surface loading rate of 330 mg Se/m(2)-day, which was higher than that in most of the conventional biological reactors. The inoculum was a microbial consortium containing both intracellular and extracellular selenium-producing bacteria, but only extracellular selenium nanoparticles were observed when the biocathode was imaged by a transmission electron microscope. Raman spectrometry further demonstrated the existence of significant Cytochrome c (Cyr c) on the cathode, an enzyme that plays a key role in extracellular electron transfer and subsequent extracellular selenium production. Quantifying factors (e.g., internal resistance and overpotential loss) that affected the current shed light on strategies for increasing the selenate removal: periodical cleaning of the cation exchange membrane and using higher electron donor concentration in the anode chamber. The electron distribution in the anodic and cathodic chambers suggested insignificant interference by methanogenesis and sulfate reduction.