Frequent human activities in estuary areas lead to the release of a large number of antibiotics, which poses a great threat to human health. However, there are very limited studies about the influence of the special natural phenomena on the occurrence and migration of antibiotics in the environment. In this study, we simulated the migration and transformation of six typical antibiotics, including oxytetracycline (OTC), tetracycline (TC), norfloxacin (NOR), ofloxacin (OFX), erythromycin (ETM), and amoxicillin (AMOX), in the environmental media from 2011 to 2019 in the Yangtze River Estuary, by using the level III multi-media fugacity model combined with the factor of tides. The simulation results showed that the most antibiotics mainly existed in soil and sediment while erythromycin were found mainly in water. The concentrations of antibiotics in air, freshwater, seawater, groundwater, sediment, and soil were 10-23-10-25, 0.1-12ng/L, 0.02-7ng/L, 0.02-16ng/L, 0.1-13ng/g, and 0.1-15ng/g respectively. Sensitivity analysis showed that the degradation rate (Km) and the soil-to-water runoff coefficient (Kl) were important model parameters, indicating that hydrodynamic conditions had a significant impact on the migration of antibiotics in various environmental phases in estuarine areas. Tide can enhance the exchange between water bodies and cause the transformation of the antibiotics from freshwater to seawater and groundwater, which improved the accuracy of the model, especially the seawater and soil phase. Risk assessments showed that amoxicillin, erythromycin, ofloxacin, and norfloxacin posed a threat to the estuarine environment, but the current source of drinking water did not affect human health. Our findings suggested that, when one would like to exam the occurrence and migration of antibiotics in environment, more consideration should be given to the natural phenomena, in addition to human activities and the nature of antibiotics.