Researchers and engineers are continuously striving to enable quicker and more individualized wastewater treatment processes control solutions for the development of process models, which is a long procedure with calibration and validation, and online data supply as they are dynamic systems introducing another level of sophistication (Sen and Randall, 2008). The existing mathematical wastewater treatment models give a forecast for treatment results under various flow and pollutant circumstances, but results still are dissatisfactory due to the changeable dynamics of pollutants, which affects the treatment systems directly. The investigation was done for an existing pharmaceutical factory wastewater treatment plant with a moving bed biofilm reactor(MBBR) process, which offers the specific advantages of the biofilm system in the treatment of high strength wastewater. The basic research was undertaken to verify a model and investigate the biodegradable and slowly biodegradable COD fraction variations influence on the model’s results.