Increased tightening of air regulations is leading more electric utilities to install flue gas desulfurization (FGD) systems. These systems produce brine containing high concentrations of nitrate, nitrite, and selenate which must be removed before discharge. The H2-based membrane biofilm reactor (MBfR) was shown to consistently remove nitrate, nitrite, and selenate at high efficiencies. The maximum selenate removal flux reached 362 mg Se m−2d−1 and was higher than that observed in earlier research, which shows continual improvement of the biofilm for selenate reduction. A low pH of 6.8 inhibited precipitation when treating actual FGD brine, yet did not inhibit removal. SO42− was not removed and therefore did not compete with nitrate, nitrite, and selenate reduction for the available H2.