The impact of hormones on ecological environments and human health is a growing concern. However, due to limitations in monitoring technologies and interdisciplinary research, most existing studies have mostly been confined to specific media (e.g., surface water) or individual pollutants. As a result, comprehensive screening and risk assessment of hormone-disrupting chemicals (HDCs) across the entire aquatic ecosystem chain in megacities remains lacking. To address this gap, we developed high-throughput sample pretreatment methods and established a suspect screening and identification strategy based on a custom-built electronic identity database for 86 HDCs. This strategy was first validated in a typical megacity. The results showed that 17.85% of 406 samples collected from four rivers and three lakes tested positive, with 24 different HDCs identified. Estrogens were detected in all matrices, while glucocorticoids showed significant concentrations in surface water, sediments, and suspended solids. Spatiotemporal analysis indicated higher concentrations in spring and summer, showed a progressive increase downstream. Source-sink analysis identified domestic sewage, medical wastewater, and aquaculture wastewater as the primary pollution sources. Hexestrol, Penbutolol, and Cortisone acetate were identified as priority control targets. This study enhances our understanding of HDCs and supports their assessment and management in global megacity aquatic ecosystems.