Awareness of residual pharmaceutically active compounds (PhACs) in aquatic ecosystems is growing as research into these pollutants increases and analytical detection techniques improve. For most pharmaceuticals analyzed, the effects on aquatic organisms have usually been investigated by toxic assays in the laboratory. However, little is known about integral analysis of pharmacokinetics in aquatic organisms and specific relations between pharmacokinetic parameters and influence factors. Moreover, the influence of the organisms involved and numerous other external factors complicates development of standard tests for environmental evaluation. Current knowledge about residual pharmaceuticals in the aquatic environment, including status, toxic effects, and pharmacokinetics in aquatic organisms, are reviewed. Based on the above, we identify major gaps in the current knowledge and some directions for future research, such as improvement of techniques to remove residual pharmaceuticals from wastewater, and the establishment of standard pharmaceutical modes of action.