Intensification refers to utilizing wastewater treatment processes that decrease chemical and energy demands, increase energy recovery, and reduce the process footprint (or increased capacity in an existing footprint) all while providing the same level of nutrient removal as traditional methods. Shortcut nitrogen removal processes; including nitrite shunt, partial nitritation/anammox, and partial denitrification/anammox, as well as low-carbon biological phosphorus removal, were critically-evaluated in this study with an overall objective of intensification of existing infrastructure. At the beginning of this study, granular sidestream deammonification was becoming well-established in Europe, but there was virtually no experience with startup or operation of these processes in North America. The experience gained from optimization of the sidestream deammonification moving bed biofilm reactor (MBBR) in this study, including the novel pH-based aeration control strategy, has influenced the startup procedure and operation of subsequent full-scale installations in the United States and around the world. Long startup time remains a barrier to the implementation of sidestream deammonification processes, but this study was the first to show the benefits of utilizing media with an existing nitrifying biofilm to speed up anammox bacteria colonization. Utilizing media with an established biofilm from a mature integrated fixed film activated sludge (IFAS) process resulted in at least five times greater anammox activity rates in one month than virgin media without a preliminary biofilm. This concept has not been testing yet in a full-scale startup, but has the potential to drastically reduce startup time. False dissolved oxygen readings were observed in batch scale denitrification tests, and it was determined that nitric oxide was interfering with optical DO sensors, a problem of which the sensor manufacturers were not aware. This led to at least one sensor manufacturer reevaluating their sensor design and several laboratories and full-scale process installations were able to understand their observed false DO readings. There is an industry-wide trend to utilize influent carbon more efficiently and realize the benefits of mainstream shortcut nitrogen removal. The A/B pilot at the HRSD Chesapeake Elizabeth Treatment provides a unique chance to study these strategies in a continuous flow system with real wastewater. For the first time, it was demonstrated that the presence of influent particulate COD can lead to higher competition for nitrite by heterotrophic denitrifying bacteria, resulting in nitrite oxidizing bacteria (NOB) out-selection. TIN removal was affected by both the type and amount of influent COD, with particulate COD (pCOD) having a stronger influence than soluble COD (sCOD). Based on these findings, an innovative approach to achieving energy efficient biological nitrogen removal was suggested, in which influent carbon fractions are tailored to control specific ammonia and nitrite oxidation rates and thereby achieve energy efficiency in the nitrogen removal goals downstream. Intermittent and continuous aeration strategies were explored for more conventional BNR processes. The effect of influent carbon fractionation on TIN removal was again considered, this time in the context of simultaneous nitrification/denitrification during continuous aeration. It was concluded that intermittent aeration was able to achieve equal or higher TIN removal than continuous aeration at shorter SRTs, whether or not the goal is nitrite shunt. It is sometimes assumed that converting to continuous aeration ammonia-based aeration control (ABAC) or ammonia vs. NOx (AvN) control will result in an additional nitrogen removal simply by reducing the DO setpoint resulting in simultaneous nitrification/denitrification (SND). This work demonstrated that lower DO did not always improve TIN removal and most importantly that aeration control alone cannot guarantee SND. It was concluded that although lower DO is necessary to achieve SND, there also needs to be sufficient carbon available for denitrification. While the implementation of full-scale sidestream anammox happened rather quickly, the implementation of anammox in the mainstream has not followed, without any known full-scale implementations. This is almost certainly because maintaining reliable mainstream NOB out-selection seems to be an insurmountable obstacle to full-scale implementation. Partial denitrification/anammox was proven to be easier to maintain than partial nitritation/anammox and still provides significant aeration and carbon savings compared to traditional nitrification/denitrification. There is a long-standing interest in combining shortcut nitrogen removal with biological phosphorus removal, without much success. In this study, biological phosphorus removal was achieved in an A/B process with A-stage WAS fermentation and shortcut nitrogen removal in B-stage via partial denitrification. / Doctor of Philosophy / When the activated sludge process was first implemented at the beginning of the 20th century, the goal was mainly oxygen demand reduction. In the past few decades, treatment goals have expanded to include nutrient (nitrogen and phosphorus) removal, in response to regulations protecting receiving bodies of water. The only practical way to remove nitrogen in municipal wastewater is via biological treatment, utilizing bacteria, and sometimes archaea, to convert the influent ammonium to dinitrogen gas. Orthophosphate on the other hand can either be removed via chemical precipitation using metal salts or by conversion to and storage of polyphosphate by polyphosphate accumulating organisms (PAO) and then removed in the waste sludge. Nitrification/denitrification and chemical phosphorus removal are well-established practices but utilize more resources than processes without nutrient removal in the form of chemical addition (alkalinity for nitrification, external carbon for denitrification, and metal salts for chemical phosphorus removal), increased reactor volume, and increased aeration energy. Intensification refers to utilizing wastewater treatment processes that decrease chemical and energy demands, increase energy recovery, and reduce the process footprint (or increased capacity in an existing footprint) all while providing the same level of nutrient removal as traditional methods. Shortcut nitrogen removal processes; including nitrite shunt, partial nitritation/anammox, and partial denitrification/anammox, as well as low-carbon biological phosphorus removal, were critically-evaluated in this study with an overall objective of intensification of existing infrastructure. Partial nitritation/anammox is a relatively new technology that has been implemented in many full-scale sidestream processes with high ammonia concentrations, but that has proven difficult in more dilute mainstream conditions due to the difficulty in suppressing nitrite oxidizing bacteria (NOB). Even more challenging is integrating biological phosphorus removal with shortcut nitrogen removal, because biological phosphorus removal requires the readily biodegradable carbon that is diverted. Partial denitrification/anammox provides a viable alternation to partial nitritation/anammox, which may be better suited for integration with biological phosphorus removal.