Methods and systems are provided for reducing ammonia partially by a denitrification process. A stream containing ammonia is contacted with oxygen to form a first product stream in low dissolved oxygen conditions. The ratio of oxygen to nitrogen is about 2.28 g O2/g N—NH3 (2.28 grams of oxygen per gram of nitrogen in ammonia) or less. The first product stream is then exposed to organic matter in an amount of 0.57 g COD/g N—NH3 (0.57 grams of chemical oxygen demand per gram of nitrogen in ammonia). This microbial reaction ultimately produces nitrogen gas, water, and carbon dioxide.