The environmental and health impacts of antibiotics (ABx) have garnered global attention. However, the issue of ABx contamination in aquatic ecosystems of densely populated megacities remains largely overlooked. Significant research gaps persist, particularly in understanding the full-chain pollution characteristics that span from urban aquatic environments to edible aquatic organisms, due in part to the lack of systematic monitoring data to support comprehensive assessments. To address this gap, this study conducts the first comprehensive screening of ABx in the aquatic ecosystems of a megacity, offering quantitative evaluations of ABx complexity and multidimensional heterogeneity. Over a one-year period, 406 samples were collected from four rivers and three lakes, and large-scale analyses identified 37 ABx compounds, with the overall detection rate of 30.05 %, with Sulfonamides (SAs), Quinolones (QNs), and Macrolides (MLs) being the most prevalent. Surface water samples contained the greatest number of ABx types, while amphibians exhibited the highest detection rate and concentrations. A pronounced increase in detections during the dry season (spring and winter) highlighted substantial spatio-temporal variation. Source-sink analysis revealed hospital effluents and wastewater treatment plants as primary pollution sources. Among the detected compounds, Nalidixic acid (NCA), Sulfamethazine (SMTZ), Flumequine (FQ), and Tylosin (TLS) posed the most significant ecological risks, with NCA identified as a priority for targeted control. This study establishes a novel framework for the high-throughput suspect screening, occurrence pattern analysis, and risk assessment of ABx in megacities worldwide.