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The occurrence of nine different types of pharmaceuticals and caffeine were analyzed in various units of three wastewater treatment plants (WWTPs) and their receiving rivers in Beijing, China. Analyte concentrations were determined using ultra performance liquid chromatograph‐tandem quadruple mass spectrometers (UPLC‐MS/MS) and multiple‐reaction monitoring. The studied pharmaceuticals and caffeine were found in all the WWTPs and receiving rivers. Their concentrations in the WWTP influents varied from 38 ng/L of sulpiride to 89.5 µg/L of caffeine, and those in the effluents ranged from 27 ng/L of sulpiride to 2.7 µg/L of erythromycin. Typically, the biological treatment appeared more effective in the removal of pharmaceuticals and caffeine than primary treatment in a WWTP. For an individual compound, the overall removal efficiency varied from one WWTP to the next. Mean values ranged from no removal of carbamazepine to 99.8% removal of caffeine. Most of the compounds in the receiving rivers were present at similar or higher concentrations compared to those in the WWTP effluents. The data set for this study does not include variations in concentrations along receiving waters because there were other point and nonpoint sources discharging to these rivers. The preliminary aquatic environmental risk assessment showed that carbamazepine, erythromycin, and trimethoprim is a potential chronic environmental risk in water bodies in Beijing, China, and is worth further investigation.