An environmental risk assessment was performed for pharmaceutical compounds present in the aquatic environment of China. Predicted environmental concentration (PEC) of the compounds were calculated according to European Medicines Evaluation Agency (EMEA) guidelines. Available ecotoxicological data compromised by applying a very conservative assessment factor (AF) were employed to calculate the predicted no-effect concentration (PNEC). The screening principle and the risk assessment were based on risk quotient (RQ), which derived from the PEC and related PNEC values. PEC results indicated that all the compounds except sulfadimethoxine and levocarnitine, should carry out phase II risk assessment in EMEA guideline. RQ values suggested that more than 36 pharmaceuticals may be imposed health threats to the aquatic environment; especially the antibiotic therapeutic class including amoxicillin, sulfasalazine, trimethoprim, oxytetracycline and erythromycin showed high RQ values. These substances with high RQ value (RQ≥1) were regarded as top-priority pharmaceuticals for control in the aquatic environment of China. However, the antibiotic substances which had low risk quotient (RQ <1), should be reassessed by its potentially induced resistance under low concentration in future.