Experimental limitations on biomass assignment in wastewater treatment units lead to an oversimplified description of the complex competing biological system. Different microorganisms are usually considered as a single entity expressed as suspended volatile solids measured by gravimetry. This work proposes a method to access autotrophic biomass fraction in a carbon/nitrogen removal system using a reduced order model. This approach allows for the determination of the autotrophic biomass fraction in response to changes in feed concentration and operational strategies in a sequencing batch reactor. The results herein presented clearly demonstrate the influence of operating conditions and batch scheduling in the resultant autotrophic fraction responsible for processes bioconversions in such a competing system. The linear relationship obtained between the autotrophic fraction and the ratio Corg/N of the load can be used for biomass assignment as well as for the development of on-line estimators.