High pH (and not free ammonia) is responsible for Anammox inhibition in mildly alkaline solutions with excess of ammonium.

Ammonium is a substrate of the anaerobic ammonium oxidation (Anammox) process but it has been suggested as a substrate-inhibitor because of the action of its unionized form, free ammonia. High pH of the medium is also an important limiting factor of the Anammox bacteria. Both effects are difficult to discriminate.