Detection of estrogenic disrupting compounds (EDCs) in drinking waters around China has led to rising concerns about health risks associated with these compounds. There is, however, a paucity of studies on the occurrence and identification of the main compounds responsible for this pollution in the source waters. To fill this void, we screened estrogenic activities of 23 source water samples from six main river systems in China, using a recombinant two-hybrid yeast assay. All sample extracts induced significant estrogenic activity, with E2 equivalents (EEQ) of raw water ranging from 0.08 to 2.40 ng/L. Additionally, 16 samples were selected for chemical analysis by gas chromatography-mass spectrometry. The EDCs of most concern, including estrone (E1), 17β-estradiol (E2), 17α-ethinylestradiol (EE2), estriol (E3), diethylstilbestrol (DES), estradiol valerate (EV), 4-t-octylphenol (4-t-OP), 4-nonylphenols (4-NP) and bisphenol A (BPA), were determined at concentrations of up to 2.98, 1.07, 2.67, 4.37, 2.52, 1.96, 89.52, 280.19 and 710.65 ng/L, respectively. Causality analysis, involving comparison of EEQ values from yeast assay and chemical analysis identified E2, EE2 and 4-NP as the main responsible compounds, accounting for the whole estrogenic activities (39.74% to 96.68%). The proposed approach using both chemical analysis and yeast assay could be used for the identification and evaluation of EDCs in source waters of China.