Occurrence of five non-steroidal anti-inflammatory drugs (salicylic acid, ibuprofen, naproxen, indomethacin and diclofenac) and three lipid regulators (bezafibrate, clofibric acid and gemfibrozil) was investigated in wastewater, sewage sludge, and river water of the urban section of the Pearl River at Guangzhou in South China. Behavior and fate of the pharmaceuticals during treatment in two sewage treatment plants (STPs) were also studied in depth by determining concentrations in the influents and effluents at major treatment units and the sewage sludge. Concentrations of the pharmaceuticals in the raw wastewater were mostly at ng L⁻¹ levels except salicylic acid whose concentrations ranged from 9.6 to 23.3 μg L⁻¹. No significant amount of the pharmaceuticals was detected in the suspended particulate matter of wastewater and sewage sludge. Salicylic acid, indomethacin, and naproxen were almost completely removed (≥99%); gemfibrozil, ibuprofen and bezafibrate were significantly removed (>75%), whereas diclofenac and clofibric acid were removed by 60–70% during treatment in the STPs. Generally, biodegradation was the governing process for elimination of the investigated pharmaceuticals. Anaerobic biodegradation was responsible for most of the removal of diclofenac whereas aerobic biodegradation also played an important role in elimination of the other pharmaceuticals except SA, which was nearly completely removed after the anoxic process. In the Pearl River, the pharmaceuticals were widely detected. Both the concentrations and detection frequency were higher in March 2008 than those in the other seasons, which may be ascribed mainly to less dilution caused by lower precipitation. Besides the STPs, urban canals directly connected with the Pearl River may also be important contributors to the pharmaceutical contamination in the river.