We report results from a systematic one-and-a-half year survey of the estrogenic isoflavones formononetin (FOR), biochanin A (BIO), daidzein (DAI), genistein (GEN), and equol in Swiss midland rivers. FOR was detected in about 90%, the other compounds in 13-56% of the weekly and fortnightly integrated flow proportional samples. Concentrations were mostly in the lower ng/L-range, with a maximum of 524 ng/L and 217 ng/L for equol and FOR, respectively. Due to dilution, concentrations were river discharge dependent with higher numbers in smaller rivers. Total isoflavone loads were in the order of a few kg/y, and occurred mainly during summertime. A complementary river water monitoring campaign throughout the country confirmed the above findings. Circumstantial evidence points to grassland as a major emission source of FOR and BIO (the main compounds in red clover) in surface waters, e.g., their absence in wastewater treatment effluents, better correlations of their loads with grassland areas than with population equivalents, similar isoflavone ratios in river water and grassland runoff. Source apportionment was less clear for DAI, GEN, and equol. The contribution of isoflavones to the total estrogenicity of surface waters is probably small, except maybe in local rural catchments without major anthropogenic activities.