In order to investigate the fate of enrofloxacin in aquatic environment, the pharmacokinetics and metabolism of enrofloxacin in silver crucian carp (Carassius auratus gibelio) were monitored after oral administration of medicated feed in the simulated aquaculture system, and the pattern of metabolism and distribution of enrofloxacin in the water body and sediment. Fish were fed enrofloxacin-medicated feed at a multiple dose of 18 mg/kg twice a day for a period of 6 days. The peak concentration (C_max) of enrofloxacin in C. auratus gibelio was intestine > kidney > muscle > gill > liver > plasma, the C_max were 14.15, 13.31, 14.15, 7.48, 7.94 mg/kg and 2.94 mg/L, respectively. The metabolite ciprofloxacin could be detected in all tissues, and the percentages of C_max of ciprofloxacin to C_max of enrofloxacin were 5.10%, 1.70%, 6.28%, 2.97%, 2.90% and 6.53%, respectively. The order of body clearance (CL_z) of enrofloxacin in the tissues was plasma > liver > intestine > gill > muscle > kidney. With the increase of administration times, the enrofloxacin concentration in water went up rapidly and the peak value (5.23 μg/L) was reached at 6 hours after the last administration; it began to decline afterwards, but the metabolite ciprofloxacin could not be detected in water. The enrofloxacin concentration in the sediment first showed an upward trend, and reached the peak value (796 μg/kg) at 240 h, then it decreased slightly and fell to 587 μg/kg at 480 h. The metabolite ciprofloxacin concentration in the sediment showed a gradual upward trend, and the residue was 382 μg/kg at 480 h. The percentage of ciprofloxacin to enrofloxacin concentration in the sediment was 27.5%-65.1%. The antibacterial residues after medicated-diet administration mainly existed in the sediment of the aquaculture ecosystem, and the percentage of antibacterial residues in the sediment was 41.86%-46.69%, and the residues eliminated slowly. We should pay close attention to the ecological safety risk of the antibacterial residues in the sediment after medicated-diet administration. This study provides technical support for scientific medicine production in aquaculture and theoretical data for ecological security assessment.