A process has steps of one or more of aerobic treatment to remove COD and nitrify a waste stream, anoxic treatment to denitrify a waste stream, anoxic treatment to remove selenium and anaerobic treatment to remove heavy metals and sulphur. The process may be used to treat, for example, FGD blow down water. The process may further include one or more of (a) membrane separation of the waste stream upstream of the anoxic digestion to remove selenium, (b) dilution upstream of the biological treatment step, (c) physical/chemical pretreatment upstream of the biological processes or dilution step to remove TSS and soften the waste stream, or (d) ammonia stripping upstream of the biological treatment steps or dilutions step. These processes may be provided in a variety of suspended growth or fixed film reactors, for example a membrane bioreactor or a fixed film reactor having a GAC bed. Processes for biological treatment of inorganic compounds in a fixed medium reactor is described including steps of one or more of maintaining desired ORP levels, optionally by controlling nutrient addition, and removing solids or gas bubbles from the medium bed.