Low content of ammonia in the treated water is one of the most important indicators of the efficiency of biological wastewater treatment. Oxidation of ammonium to nitrate (nitrification) is carried out by nitrifying bacteria, which have low growth rates and are very sensible to certain unfavorable technological factors, such as low oxygen concentration and toxicants). To stabilize the number of nitrifying bacteria, increasing their activity in bioreactors with activated sludge and, therefore, to achieve stable and efficient removal of nitrogen compounds, various techniques are used, one of which is bioaugmentation technology. Bioaugmentation implies addition of the necessary microorganisms or creation of the conditions favoring their development in order to increase the specific activity of biological systems, such as activated sludge. In the Engineering and Technological Centre of JSC ‘Mosvodokanal’ for the first time in world practice, we studied the efficiency of nitrification in a plant operating under the scheme of the University of Cape Town process, in combination with an additional bioaugmentation reactor. Activated sludge in the reactor was enriched with nitrifying bacteria. At higher ammonium loads, which were modeled by adding the liquid phase of digested sludge, the main line did not remove ammonium to the maximum permissible concentration for fishery water bodies. The use of a bioaugmentation reactor resulted in ammonium concentration decrease from 40–50 to 0.4 mg N-NH4/l. This approach increased the stability of the activated sludge nitrifying bacteria to toxicants (thiourea).