Nitrification is an essential microbial process in the global nitrogen cycle. The first step of nitrification is ammonia oxidation which is achieved by bacteria and archaea and is crucial in decreasing ammonia concentrations that are persistently high in wastewater. This study examined the composition, abundance and identity of the microbial community in activated sludge with a focus on characterizing ammonia oxidizing bacteria and archaea in a full-scale municipal wastewater treatment plant (MWTP). Specifically, two pharmaceutical compounds Tetracycline and Ibuprofen, and their effects on the community composition of bacteria and protozoa in activated sludge was investigated using PCR coupled with denaturing gradient gel electrophoresis (DGGE). In addition, the composition, abundance and activity of the ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) were analyzed from aerobic activated sludge, recycled sludge and anaerobic digesters of the Humber MWTP using molecular techniques such as PCR, Quantitative PCR, Reverse Transcription-PCR and DGGE. The findings demonstrated that Tetracycline did not appear to alter community composition of bacteria in the activated sludge, rather, the operational parameters of the sequencing batch reactors such as feeding rates and SRT have shown to alter the richness of bacterial communities. However, Ibuprofen affected some members in the protozoan community in activated sludge. In the full-scale Humber MWTP using the conventional activated sludge system, the aeration tanks contained 1.8 × 105 copies of the AOB amoA gene per 100 ng of DNA. In contrast, the anaerobic digester tanks contained 7.3 × 102 copies of the AOA amoA gene per 100ng of DNA. This study also found that AOB were dominant in activated sludge samples, regardless of the operational parameters. The quantification of cDNA transcripts of the amoA gene also indicated that AOB may be more active than AOA in the activated sludge system. Overall, it appears that AOA are very niche specific and thrive in very low oxygenated environments, while AOB proliferate and play a major role in aerobic ammonia oxidation occurring in MWTPs.