Methods of controlling a nitrification reaction in a biological nitrogen removal reactor to favor partial nitrification of ammonia to nitrite instead of complete oxidation of ammonia to nitrate are disclosed. In some embodiments, the methods include the following: maintaining a pH in the reactor within a range that promotes growth of ammonia oxidizing bacteria; maintaining a concentration of dissolved oxygen in the reactor within a range that limits the ammonia oxidizing bacteria from completing nitrification; selecting an operational solids retention time within a range suitable for maintaining increasing concentrations of the ammonia oxidizing bacteria in the reactor while reducing concentrations of nitrite oxidizing bacteria in the reactor; and increasing a concentration of free ammonia in the reactor thereby inhibiting growth of the nitrite oxidizing bacteria in the reactor.
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