A pilot scale biological nutrient removal (BNR) process, batch experiments and modeling exercises were employed to investigate the removal and biotransformation of trimethoprim (TMP) in a BNR activated sludge process. The concentrations of the active microbial groups – ammonia oxidizing bacteria (AOB), ordinary heterotrophic organisms (OHOs) and polyphosphate accumulating organisms (PAOs) – in the BNR bioreactor were quantified through modeling of the pilot bioreactor. The overall TMP removal efficiency for the pilot BNR process was 64 ± 14% while the TMP biotransformation efficiencies in the anaerobic, anoxic and aerobic zones were 22 ± 20%, 27 ± 8% and 36 ± 5% respectively. Batch tests with and without nitrification inhibition showed that AOB played a role in the biotransformation of TMP in BNR activated sludge. A pseudo first order model which incorporated the contributions of PAOs, OHOs and AOB to the overall biodegradation of TMP was found to describe the biodegradation of TMP in batch tests with and without nitrification inhibition. This model showed that PAOs, OHOs and AOB contributed towards the biotransformation of TMP in aerobic BNR activated sludge with the biotransformation rate constants following the trend of kAOB > kOHOs > kPAOs.