Information about the biotransformation of organic micropollutants (OMPs) in biological systems is currently scarce, particularly in anoxic environments. A lab-scale reactor was set up to elucidate which is the biological mechanism driving OMPs biotransformation in heterotrophic denitrifying conditions. The influence of microbial composition on the OMPs removal was analysed. Increasing levels of nitrate loading rates were applied during the study in order to analyse cometabolism. In terms of OMPs, high removal efficiency was achieved for compounds such FLX and SMX, whereas moderate removal was achieved for some antibiotics (ERY, ROX, TMP), the anti-depressant drug CTL or the natural hormones. Other OMPs, like DCF or CBZ were recalcitrant. Removal due to cometabolism was detected for BPA, ERY, ROX and CTL.