Intensive economic development causes the risk of introducing the so-called emerging contaminants (EC) into the environment. This group of contaminants includes pharmaceuticals, including non-steroidal anti-inflammatory drugs (NSAIDs), the consumption of which is steadily increasing in Poland as well as worldwide. Such specific contaminants may also cause problems at the stage of biological treatment of wastewater, especially in individual systems that are sensitive to changes in wastewater composition. The study examined an onsite wastewater treatment system based on the activated sludge technology, to which three different pharmaceuticals were dosed in the quantities normally used in therapy. The operation of the biological reactor under these conditions was analysed by comparing contamination indicators at the inlet and outlet of the treatment plant at different doses of pharmaceuticals. It was found that the doses used did not significantly worsen the effects of wastewater treatment, except for paracetamol, which at a dose above 1000 mg/d caused a slight reduction in the efficiency of the facility. The dosed pharmaceuticals also did not deteriorate the sedimentation properties of the activated sludge. Although typical doses of pharmaceuticals do not interfere with the operation of the biological reactor, residual substances and their metabolites may be released into the environment; it is therefore reasonable to consider the introduction of an additional treatment stage to remove micropollutants from the wastewater.