Mathematical modelling plays a key role in understanding and quantifying uncertainties of emerging pollutants in wastewater treatment processes (WWTPs). This paper presents for the first time a simplified emerging pollutant pathway that incorporates two pathways to sequestration. It develops deterministic and stochastic ordinary differential equations to gain insight into the fate and behaviour of a case study pharmaceutical, with particular focus on sorption to the solid phase, as well as the nature of the experimentally measured solid parent compound. Statistical estimation and inferential procedures are developed and via a proof-of-concept examination, the study explores the transformation pathways of the bioactive chemicals (BACs) in the bioreactor, which is the heart of the WWTP. Simulations of 17 alpha-ethinylestradiol (EE2) as a case study, show good agreement with data. The results suggest that the measured EE2-parent concentration in the solid phase is very similar to the model-based sequestered (rather than adsorbed) EE2-parent concentration. (C) 2019 Elsevier Ltd. All rights reserved.