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As a new and ubiquitous trace organic pollutant, endocrine-disrupting compounds (EDCs) can cause endocrine-disrupting effects on organisms even at low levels. However, little information is available on the resource and assessment of EDC risks in the water environment. The study area was selected based on the paucity of information on the pollution status of inland lakes. Wuhan has numerous and diverse types of lakes which receive micropollutants from different pathways. In this study, the spatial distribution, occurrence, quantity and ecological risks of EDCs in 12 lakes were investigated. Five EDCs, including 17-alpha-ethinylestradiol (17α-EE2), estrone (E1), β-estradiol (β-E2), estriol (E3) and bisphenol A (BPA) were detected in surface waters. The distribution of EDC content in the lakes was ordered as follows: exurban zone < suburban area < urban areas. The pollution sources in remote lakes mainly included agricultural and aquaculture wastewater, while those in suburban and urban areas included domestic or industrial wastewater. Areas with higher EDC content were frequently related to agricultural activities, aquaculture water or dense populations. Water quality parameters, including dissolved oxygen, pH and water temperature, were significantly related to the occurrence and distribution of EDCs in the lakes. Risk assessment demonstrated that the occurrence of EDCs posed minimum to medium risk to aquatic organisms in the lakes. The results showed that the lakes faced a threat hormone pollution though it was at lower doses and, thus, the ecological risk of EDCs should be considered in future environmental policies and decisions in China.