In recent years, the widespread application of antibiotics has raised global concerns, posing a severe threat to ecological health. In this study, the occurrence, source, and ecological risks of 39 antibiotics belonging to 5 classes in mangrove sediments from Lianzhou Bay, China, were assessed. The total concentrations of the antibiotics (∑39 antibiotics) ranged from 65.45 to 202.24 ng/g dry weight (dw), with an average of 142.73 ± 36.76 ng/g dw. The concentrations of these five classes of antibiotics were as follows: Sulfonamides (SAs) > Tetracyclines (TCs) > Fluoroquinolones (QUs) > Penicillin (PCs) > Macrolides (MLs). The spatial distribution of antibiotics varied as high tidal zone > middle tidal zone > low tidal zone. The total organic carbon (TOC), pH, nitrate (NO3--N), and nitrite (NO2--N) of the sediment significantly influenced the distribution of antibiotics (p < 0.05). A source analysis identified untreated sewage from aquaculture as the primary source of antibiotics in the local mangrove. A risk assessment revealed that ciprofloxacin, norfloxacin, ofloxacin of QUs, and tetracycline of TCs exhibited medium risks to algae in certain sampling sites, while other antibiotics exhibited low or no risks to all organisms. Nevertheless, the total risk of all the detected antibiotics to algae was medium in 95% of the sites. The overall ecological risk level of antibiotics in the middle tidal zone was slightly lower than in the high tidal zone and the lowest in the low tidal zone. In summary, the experimental results provided insights into the fate and transport behaviors of antibiotics in mangrove sediments from Lianzhou Bay.