The paper summarises the definition of an extended biokinetic model dedicated to micropollutant degradation in wastewater treatment and the parameter estimation methodology for this model. Additionally it describes results on experimental parameter estimation for two target micropollutants, naphthalene disulfonate (2,6-NDSA) and benzothiazole sulfonic acid (BTSA). Subsequently the parameterised model is applied to real operational data from two laboratory-scale (MBR) installations. The work presents the full chain of theoretical model development, model analysis and practical application to case study data for micropollutants.