Hospital effluents are important sources for the release of pharmaceuticals into the environment. Metronidazole (MTZ) is one of the most popular antimicrobial agent, widely used in veterinary and human medicine. This study aims to determine the concentrations of MTZ in the effluent of hospitals and to evaluate ecotoxicological risk for aquatic organisms. Grab samples were taken from the effluents of 15 large hospitals in Isfahan City (Iran) and MTZ concentrations were analyzed using HPLC-UV. Average daily MTZ prescriptions for patients in each hospital was also determined. MTZ was detected in effluents of all 15 hospitals in the range of 0.3 to 9.5 µg/L (mean = 4.8 ± 6.4 µg/L). A significant correlation was observed between MTZ concentration in hospital effluent and MTZ prescription as well as the hospital beds. Ecological risk assessment showed MTZ contamination of hospital effluent from 7 of 15 hospitals had median risk (risk quotient of 0.1 to 1) for green algae (Chlorella sp.) while the effluent of all hospitals had minimal risk (risk quotient <0.1) for gram-negative bacteria (Vibrio fischeri) and aquatic crustaceans (Daphnia magna). It is necessary to develop efficient treatment methods for the removal of MTZ from the hospital effluents before discharging them into the municipal wastewater systems.