Pharmaceuticals and particularly antibiotics can harm sensitive aquatic species. Their occurrence in urban wastewater systems is the consequence of five successive processes: (i) ingestion of the substance, (ii) accumulation in the urine, (iii) excretion, (iv) degradation in the sewer system and (v) transport to the wastewater treatment plant (WTP). These processes were included in an integrated model that can be used to assess the dynamics of pharmaceuticals at a WTP inlet. First, information on sales data, posology, pharmacokinetics and toilet flushing frequency were combined to create a source model of pharmaceuticals entering a sewer system. This production function was then coupled with a transport/degradation model to simulate concentrations of pharmaceuticals at a WTP inlet. In an example application, the full model was applied to simulate the concentration of the antibiotic ciprofloxacin on an hourly time scale. In this application, the model was calibrated and validated for a case study at a WTP in Lausanne, Switzerland. Validation of the integrated approach was successful despite the high variability evident in the model results. This modeling approach has potential use in pollution management and epidemiology related to wastewater.