Wastewater, for example flue gas desulphurization blowdown water, containing soluble selenium is treated in a bioreactor. Microorganisms in the reactor reduce the selenium to elemental selenium, which is insoluble. The elemental selenium is discharged from the reactor in waste sludge also comprising biomass and other suspended solids. Non-microbial suspended solids are removed by way of acid dissolution followed by de-watering. The remaining sludge is burned at a temperature below the selenium oxidation temperature to remove biomass while leaving selenium particles behind.