Methods and systems for controlling a denitrification reaction in a biological nitrogen removal reactor including denitrifying bacteria to favor denitratation of nitrate to nitrite and limit denitritation of nitrite to nitrogen gas are disclosed. pH, dissolved oxygen levels, solids retention time, and chemical oxygen demand to nitrogen ratio are controlled to favor this reaction. Wastewater or contaminated groundwater including concentrations of ammonium and nitrate are continuously fed to the biological nitrogen removal reactor along with a source of carbon and electrons as an influent, which is treated to form a nitrite effluent. The nitrite effluent may then be fed to an anammox reactor including anammox bacteria for production of nitrogen gas. The system may be operated under substantially anoxic conditions, which provides significant cost savings without sacrificing efficiency or productivity compared to traditional wastewater treatment systems and processes.