The efficiency of the bioaugmentation of nitrifying bacteria into biofilm microbiocenosis with 30 days of continuous biofiltration of a solution of municipal model wastewater has been assessed. The laboratory setup consisted of two parallel operating biofilters. Cultures of ammonium-oxidizing and nitrite-oxidizing bacteria of the Nitrobacter genus were sequentially introduced into one of them after the initial period. It was established that the bioaugmentation of ammonium-oxidizing bacteria into the biofilm microbiocenosis led to an increase in the efficiency of the removal of ammonium nitrogen by an average of 1.6 times as compared to the control biofilter. The subsequent bioaugmentation of nitrite-oxidizing bacteria caused an increase in the amount of nitrates in purified water by an average of two times. The bioaugmentation of nitrifying bacteria in the biofilm microbiocenosis intensified the nitrification process. The quantitative and qualitative identification of microorganisms via fluorescence in situ hybridization showed an increased number of nitrifying microorganisms in the biofilm of the experimental biofilter and a correlation between this characteristic and the biotransformation of nitrogen compounds, which confirms the efficiency of the introduction of microorganisms into the biofilm.