The study evaluated the most efficient biological nitrogen removal (BNR) process in four full-scale municipal wastewater treatment plants (WWTPs) by using BioWin, a simulation software based on the activated sludge model (ASM). A series of experiments were conducted to determine the kinetic and stoichiometric parameters for the ASM. Results indicated that autotrophic maximum specific growth rates in the studied WWTPs were generally higher compared to previous findings, likely due to their low COD/N ratios, emphasizing the importance of local parameterization. Continuous water quality monitoring in each plant was employed to validate the model. Dynamic simulation results indicated that the error remained within an acceptable range, with a mean relative error of less than 20%, confirming the reliability of ASM parameters derived from batch experiments. Subsequently, various operational scenarios were analyzed to determine the optimal BNR process for each plant, considering influent flow rate, internal recycling, and methanol addition. Simulation outcomes suggested that O/A (oxic/anoxic) operation is preferable for plants with low organic content (COD = 60–110 mg/L), considering both operational costs and total nitrogen removal rate. Conversely, A/O (anoxic/oxic) operation might be advantageous for plants with higher influent organic matter (COD = 200 mg/L).