In accordance with the principles of the present invention, methods and apparatuses are provided for practically complete removal of one or more electron acceptors (excluding oxygen) from waters of various origins, while ensuring that an added excess of external carbon is also practically completely removed using biological treatment. A method applies to waters that contain the target electron acceptor and a deficiency of carbon. One application of this method is the practically complete removal of nitrate from domestic wastewater (septic wastewater) while practically completely removing the added excess of external carbon, thus practically eliminating any increase of the biological oxygen demand of the water. Another method applies to waters that contain constituents that are potentially convertible to the target electron acceptor and may contain original carbon. One example of this method is aerobic pre-treatment of a water to yield nitrate and a deficiency of carbon, resulting in a water amenable to treatment via the previous method.