The present study is the first comprehensive monitoring of 13 selected endocrine disrupting compounds (EDCs) in untreated urban and industrial wastewater in Serbia to assess their impact on the Danube River basin and associated freshwaters used as sources for drinking water production in the area. Results showed that natural and synthetic estrogens were present in surface and wastewater at concentrations ranging from 0.1 to 64.8 ng L−1. Nevertheless, they were not detected in drinking water. For alkylphenols concentrations ranged from 1.1 to 78.3 ng L−1 in wastewater and from 0.1 to 37.2 ng L−1 in surface water, while in drinking water concentrations varied from 0.4 to 7.9 ng L−1. Bisphenol A (BPA) was the most abundant compound in all water types, with frequencies of detection ranging from 57% in drinking water, to 70% in surface and 84% in wastewater. Potential environmental risks were characterized by calculating the risk quotients (RQs) and the estrogenic activity of EDCs in waste, surface and drinking water samples, as an indicator of their potential detrimental effects. RQ values of estrone (E1) and estradiol (E2) were the highest, exceeding the threshold value of 1 in 60% of wastewater samples, while in surface water E1 displayed potential risks in only two samples. Total estrogenic activity (EEQt) surpassed the threshold of 1 ng E2 L−1 in about 67% of wastewater samples, and in 3 surface water samples. In drinking water, EEQt was below 1 ng L−1 in all samples. Display omitted •Occurrence and risk assessment of 13 EDCs was evaluated in three water types from Serbia.•BPA was the most abundant compound riched 338 ng L−1 in analyzed wastewater samples.•EEQt surpassed threshold of 1 ng L−1 in 67% (10%) of waste (surface) water samples.•EDCs present in drinking water might not induce negative effects on human health.