The New York City Department of Environmental Protection (NYCDEP) has developed and is utilizing a unique sidestream treatment process that provides for nitrogen removal from high ammonia anaerobically digested sludge dewatering centrate, while producing predominantly nitrite as the ammonia oxidation product (Katehis, 2002; Fillos, 2005). The biomass produced in the sidestream process is then utilized to bioaugment the main plant’s activated sludge reactors, resulting in significant nitrogen removal in the main plant. Nitrite is also a dominant product of ammonia oxidation in the main plant, providing for nitrogen removal from the main plant flow, whilst utilizing only a fraction of the aeration and carbon requirements associated with conventional nitrification and denitrification. In order to allow for the optimal deployment of the process in other NYCDEP facilities a combined bench and full scale evaluation was conducted, followed by process modeling using initially a two-step nitrification model (using the Grey Box Model Builder) in BioWin 2.1, then the two step beta version of the BioWin 3 model. The BioWin v3 model allows for modeling of each of the two primary stages of nitrification (ammonia oxidation and nitrite oxidation) separately and was necessary to simulate the process as nitrite was the dominant product of the oxidation reduction. One of the concerns in the deployment of this innovative process is the ability to demonstrate and quantify the improvement due to the centrate sidestream reactor. To supplement the data collected at the plant, a BioWin model of the process was developed, using a combination of bench scale experiments and the plant process performance evaluation.