The estrogenic activity in water at various localities on Lake Biwa-Yodo River, a representative watershed in Japan, was measured using a recombinant yeast that expresses the human estrogen receptor. The yeast bioassay revealed that the activities of 13 water samples had an average value of 14 pmol/L (3.8 ng/L) (17beta-estradiol equivalent) with a very wide range from 0 to 72 pmol/L (0-19.6 ng/ L), and two of the samples had prominent levels of activity (72 pmol/L (19.6 ng/L) and 56 pmol/L (15.2 ng/L)). We analyzed these two samples with instrumental approaches. A high-performance liquid chromatogram profile showed that the strong activity in one sample, which was collected just downstream of a sewage-treatment plant, would be due to 17beta-estradiol and estrone, whose source is considered to be human urine contained in the effluent of the plant. The activity in the other sample, which was obtained from a tributary river in a primarily residential area with some industrial development (i.e., Osaka City), however, did not correspond to 17beta-estradiol, estrone, or synthetic chemicals known as estrogenic. Analysis of a fraction with estrogenic activity by liquid chromatography-mass spectrometry (LC-MS) provided evidence that the activity in the water sample resulted from the presence of genistein, an isoflavone compound of plant origin.