The complexity of biological activities and the number of process variables important to nutrient removal in advanced activated sludge wastewater treatment plants (WWTPs) require the use of process simulation. Process simulation can help engineers evaluating different treatment processes and designing the best biological nutrient removal (BNR) process. It can help operators optimize their plant performance and, at the same time, reduce their operating cost associated with aeration and methanol addition. In this paper, a new process model for the continuous-flow sequencing reactor (CSR)—which was developed by Hydromantis for its GPS-X process simulator—will be described. Also, model development and calibration of the Roth Lane WWTP (which uses the CSR process) will be first presented and followed by simulations designed to predict plant performance at different flow and loading conditions.