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Pharmaceuticals in wastewater have clearly raised concern and a broad range of analytical methods has been used to assess the risk as accurately as possible. The aim of our study was to measure and compare the concentrations of atorvastatin, bisoprolol, carbamazepine, ciprofloxacin, clofibric acid, diclofenac, fluoxetine, metoprolol, and sertraline in wastewater samples taken from one municipal and one hospital wastewater treatment plant in Slovenia and to predict the potential environmental burden using the risk quotient. In both effluents only clofibric acid and fluoxetine were not detected. The measured concentrations of the remaining seven pharmaceuticals varied between the ng L−1and the μg L−1range. Hospital effluent showed higher concentrations, except for diclofenac and carbamazepine. However, high risk quotient was found only for ciprofloxacin and diclofenac in both municipal and hospital effluent. In conclusion, our method can provide a useful tool for systematic monitoring of pharmaceuticals commonly found in wastewater, which will enable a reliable assessment of the risks for the aquatic biota and humans. Knowing the risks will help to plan wastewater treatment and preserve our environment.