High concentrations of soluble selenium, selenate and selenite, have acute and chronic toxicity toward living things. With the aim of developing a biological process for selenium removal, the effects of a variety of parameters on the reduction of soluble selenium by a Bacillus sp. strain SF-1, which is capable of reductively transforming selenate into selenite and, subsequently, into nontoxic insoluble elemental selenium, were studied. The bacterial strain could effectively reduce 20 mM of selenate to selenite and 2 mM of selenite to elemental selenium in the presence of an appropriate carbon source and in the absence of oxygen. The reduction rate of selenate to selenite was much higher than that of selenite to elemental selenium, resulting in the transient accumulation of selenite during selenate reduction. The selenate reduction rate increased with increases in the selenate concentration up to 20 mM, while the rate of selenite reduction decreased sharply at selenite concentrations of more than 2 mM. The elemental selenium transformed from selenate via selenite was found both inside and outside the cells. Bacillus sp. SF-1 was able to utilize a variety of organic acids or sugars as a carbon source in selenate reduction. Although the copresence of sulfate did not inhibit selenate reduction, it was completely inhibited by some other oxyanions, including nitrate. A model sequencing batch system using the bacterial strain was developed and exhibited good performance in the treatment of wastewater containing high concentrations of selenate.