In light of the estrogenic potentials and the recent concentration levels found for six phytoestrogens in surface waters, detailed monitoring and assessment of potential input sources are required. An accurate, precise, and sensitive HPLC-MS/MS analytical method incorporating five (13)C 3-labeled internal standards for the quantification of these plant estrogens in various aqueous environmental samples is presented here for the first time. The compounds investigated included biochanin A, daidzein, equol, formononetin, genistein, and coumestrol. The use of [ (13)C 3]biochanin A, [ (13)C 3]daidzein, [ (13)C 3]equol, [ (13)C 3]formononetin, and [ (13)C 3]genistein ensured an accurate quantification of the target analytes unaffected by matrix effects and analyte losses. Absolute method recoveries for all analytes ranged from 63 to 105%, from 63 to 99%, and from 73 to 133%, relative recoveries from 90 to 132%, from 89 to 139%, and from 89 to 115%, method detection levels from 0.5 to 2.7 ng/L, from 0.5 to 2.6 ng/L, and from 0.4 to 11.0 ng/L, and precision from 1 to 19%, from 1 to 16%, and from 1 to 11% in drainage water, river water, and WWTP effluent, respectively. The validated analytical method was applied in investigating the emission of the phytoestrogens via drainage water from a pasture containing 43% red clover ( Trifolium pratense) and in monitoring their occurrence in Swiss surface waters. Isoflavone concentrations ranging from 4 to 157 ng/L and up to 22 ng/L were found in drainage and river water, respectively.