As a result of the widespread use of antibiotics, a large amount of excretion from human and animals containing antibiotic residues was discharged into the environment with wastewaters and manures, leading to potential adverse effects on ecosystem health. To understand the environmental fate of antibiotics, a dynamic level IV fugacity model was established here by introducing the novel process of nondiffusive wastewater irrigation from water to soil, and applied to a large-scale water-scarce region, the megacity Beijing. Furthermore, a Monte-Carlo based risk assessment approach was employed to evaluate the potential risks posed by antibiotics in water, sediment and soil, combined with the soil-water equilibrium partitioning method. Model validation, sensitivity and uncertainty analysis suggests that the fugacity model can successfully simulate the reported concentration data within an average difference of 0.2 logarithmic units. Results showed that more than one hundred tonnes of antibiotics were estimated to be discharged into the environment of Beijing in 2013, and, resulted in high antibiotics levels and posed high potential risks on the aquatic environment. On the other hand, although wastewater irrigation increased the antibiotics concentrations in soil and even dominated the total transfer fluxes, the overall risk levels of antibiotics in the soil were acceptable.