Antibiotics are largely applied in aquaculture to increase production and control diseases, while how the antibiotics used in pond farming influence the distribution of antibiotics in receiving water seasonally is still not well understood. In this study, the variations of 15 frequently used antibiotics in Honghu Lake and surrounding ponds were investigated seasonally to figure out the impact of pond farming on antibiotics distributions in Honghu Lake. Results showed that the antibiotic concentrations in fish ponds ranged from 11.76 to 389.8ng/L, while in crab and crayfish ponds were lower than 30.49ng/L. The predominant antibiotic in fish ponds was florfenicol, followed by sulfonamides and quinolones, with generally low concentrations. Sulfonamides and florfenicol were the main antibiotics in Honghu Lake, affected by the surrounding aquaculture water partially. The antibiotics residue in aquaculture ponds showed obvious seasonal characteristics, with the lowest in spring. From summer, the concentrations of antibiotics in aquaculture ponds gradually increased and reached a peak in autumn, and the seasonal variation of antibiotics in the receiving lake was also related to the antibiotics in the aquaculture ponds. Risk assessment analysis showed that antibiotics such as enrofloxacin and florfenicol in fish ponds posed a medium and low risk to algae, and Honghu Lake acted as a natural reservoir of antibiotics and poses increased risks to algae. In general, our study demonstrated that aquaculture represented by pond farming brought significant risks of antibiotic pollution to natural water bodies. Therefore, reasonable control of the fish antibiotics usage in autumn and winter, as well as the rational use of antibiotics in aquaculture and the use of antibiotics before pond cleaning, is required to reduce the migration of antibiotics from aquaculture surface water to the receiving lake.