The occurrence, removal and ecotoxicological assessment of 21 pharmaceutically active compounds (PhACs) including antibiotics, analgesics, antiepileptics, antilipidemics and antihypersensitives, were studied at four municipal wastewater treatment plants (WWTP) in Chongqing, the Three Gorges Reservoir Area. Individual treatment unit effluents, as well as primary and secondary sludge, were sampled and analyzed for the selected PhACs to evaluate their biodegradation, persistence and partitioning behaviors. PhACs were identified and quantified using high performance liquid chromatography/tandem mass spectrometry after solid-phase extraction. All the 21 analyzed PhACs were detected in wastewater and the target PhACs except acetaminophen, ibuprofen and gemfibrozil, were also found in sludge. The concentrations of the antibiotics and SVT were comparable to or even higher than those reported in developed countries, while the case of other target PhACs was opposite. The elimination of PhACs except acetaminophen was incomplete and a wide range of elimination efficiencies during the treatment were observed, i.e. from "negative removal" to 99.5%. The removal of PhACs was insignificant in primary and disinfection processes, and was mainly achieved during the biological treatment. Based on the mass balance analysis, biodegradation is believed to be the primary removal mechanism, whereas only about 1.5% of the total mass load of the target PhACs was removed by sorption. Experimentally estimated distribution coefficients (<500 L/kg, with a few exceptions) also indicate that biodegradation/transformation was responsible for the removal of the target PhACs. Ecotoxicological assessment indicated that the environment concentrations of single compounds (including sulfadiazine, sulfamethoxazole, ofloxacin, azithromycin and erythromycin-H2O) in effluent and sludge, as well as the mixture of the 21 detected PhACs in effluent sludge and receiving water had a significant ecotoxicological risk to algae. Therefore, further control of PhACs in effluent and sludge is required before their discharge and application to prevent their introduction into the environment. (C) 2013 Elsevier B.V. All rights reserved.