Ammonia oxidizing archaea (AOA) have been found as a key player in ammonia oxidation. Over the past decade, AOA have been shown in some cases to outnumber ammonia oxidizing bacteria (AOB) in marine, terrestrial and aquatic environments, and to participate in nitrification. In this dissertation research, AOA along with AOB were examined for their presence and activities in wastewater treatment plants (WWTPs), and water treatment plants (WTPs) employing different disinfectants and their distribution systems (DSs). Firstly, this research investigated the abundance and seasonal variation of AOA and AOB by quantitative polymerase chain reaction targeting the ammonia monooxygenase subunit A gene (amoA) in the biofilm from trickling filters (TFs) and a moving bed bioreactor (MBBR) employed separately at two WWTPs. AOA and AOB dominated nitrifying cultures from the same WWTPs were selected using specific inhibitors, and investigated for nitrification activity. Secondly, this research examined copper inhibition of nitrification by attached and suspended growth ammonia-oxidizing cultures containing different fractions of AOA. The third and final research part investigated AOA and AOB abundance and nitrification activity in different treatment steps of WTPs practicing chloramination and chlorination and distal and proximal zones of their DSs. A laboratory experiment simulating DS conditions with chorine and chloramine was conducted to understand the effects of disinfectant concentration and type, and water temperature on AOA and AOB populations and activity. AOA were dominant in the nitrifying TF (NTF) and MBBR, while AOB dominated in the biochemical oxygen demand TF. AOA and AOB were more abundant during warm months. In-situ nitrification activity showed the oxidation of ammonia to nitrite decreased when AOA populations from the NTF and MBBR were inhibited, demonstrating that AOA contributes to nitrification. Nitrification by the cultures heavily dominated by AOA were less inhibited by copper than the cultures with less AOA dominance. In WTP systems studied, more AOA were observed in chloraminated DS compared to chlorinated DSs. More AOA and AOB were detected in the distal zones than the proximal zones of DSs suggesting that AOA and AOB grew in the distribution systems. AOA had longer inactivation time under cold water temperature compared to AOB.