Abstract The aim of this work was to study the biological removal of pharmaceutical compounds in rotating biological contactors (RBCs) under continuous operation. A two-stage RBC was used, providing a total surface area of 1.41m2. Four pharmaceuticals of different therapeutic classes; caffeine, sulfamethoxazole, ranitidine and carbamazepine, were studied. Six experimental scenarios were applied to the RBC-system by varying substrates’ loadings (12–54gCOD/d), volumetric flow rate (2–5L/d), and pharmaceuticals’ concentration (20–50μg/L). The different conditions resulted to different solid retention times (SRT: 7–21d) in each scenario. The increase of SRT due to variations of the operating conditions seemed to have a positive effect on pharmaceuticals’ removal. Likewise, a negative correlation was observed between substrates’ loading and pharmaceuticals’ removal. An increase of initial pharmaceuticals’ concentration resulted to decrease of SRT and pharmaceuticals’ removal, suggesting a toxic effect to the biofilm. The maximum removals achieved were greater than 85% for all pharmaceuticals. Finally, a mathematical model which includes biofilm growth, substrates’ utilization and pharmaceuticals’ elimination was developed. The model predicts the contribution of sorption and biodegradation on pharmaceuticals’ elimination taking into account the diffusion of pharmaceuticals inside biofilm.