Bacterial communities constitute one of the principal drivers for engineered technologies and processes in water and wastewater treatment. Over the past decade or so, using advanced molecular biology techniques, it has become possible to interrogate these engineered systems to determine the identity of the main microbial protagonists therein. In this dissertation research, the application of these techniques has been extended to develop molecular biomarkers that specifically examine the microbial ecology, activity and abundance of aerobic and anaerobic ammonia oxidizing bacteria in engineered drinking water and wastewater systems. The overall goals of this dissertation research were (1) to develop and apply molecular biomarkers that link microbial community structure and activity to anaerobic ammonium oxidation (anammox) process performance in a 2-stage bioreactor fed with actual anaerobic digestion centrate from a full-scale operational wastewater treatment facility in New York City, and (2) to investigate the suitability of molecular biomarkers for monitoring nitrification episodes and to examine the impact of alternating chloramination-chlorination over two consecutive years on the microbial ecology and abundance of AOB in a drinking water system. Based on these studies, it was possible to successfully link the microbial ecology, gene expression and N-removal in the test anaerobic ammonia oxidation (anammox) bioreactor. The 'predictive' potential of molecular biomarkers based on expression of hydrazine oxidoreductase and the intergenic spacer region of the 16S-23S ribosomal RNA genes was also demonstrated. Further, it was shown that reactor operating strategies contribute more to the microbial ecology of anammox reactors than the inocula to these reactors themselves. Using similar techniques and biomarkers, the presence of novel ammonia oxidizing bacteria was discovered in a full-scale drinking watershed, subjected to alternating chloramination-chlorination. Additionally, it was determined that free-chlorination did not have long-term impacts on the population size or structure of the ammonia oxidizing bacteria. Therefore, alternate strategies for chlorine and chloramine based drinking water disinfection have been suggested.