In one embodiment, a system includes first anoxic moving bed biofilm reactor (MBBR) configured to receive a fluid containing selenium and to process the fluid via a first biofilm disposed on a first media to produce a first MBBR fluid by removing nitrogen from the fluid. The system further includes a second anoxic MBBR fluidly coupled to the first MBBR to receive the first MBBR fluid and to process the first MBBR fluid via a second biofilm disposed on a second media to produce a selenium enriched fluid, followed by a solid-liquid separation system to remove selenium in solid form as sludge and produce a treated effluent containing equal to or less than 5 micrograms of selenium per liter. The system includes a plurality of first sensors and first actuators disposed on the first MBBR, and a plurality of second sensors and second actuators disposed on the second MBBR.