Natural estrogens such as 17α-estradiol (E2α), 17β-estradiol (E2β), estrone (E1), and estriol (E3), released to surface waters from both urban and agricultural sources, are endocrine disrupting for fish. Here, we assess the prevalence of livestock farming derived natural estrogens in tributaries and ponds in the agriculturally dominated catchment of Lake Baldegg, Switzerland. Passive samplers were deployed in the main tributary and daily time-proportional water samples were collected in five tributaries for 30 days at the beginning of the vegetation period. Furthermore, we took grab samples of 12 ponds in the catchment. Aqueous samples were liquid–liquid extracted, derivatized, and analysed with LC-MS/MS and stream water samples additionally with ERα-CALUX, a bioassay for assessing total estrogenic activity. Natural estrogens were regularly detected, with mean concentrations ranging from below the limit of detection to 0.55 ng L⁻¹ for E2β and E1, respectively, and passive sampling and bioassay results largely confirmed these findings. Monte Carlo simulated mean natural estrogen concentrations underestimated measured ones by a factor of three to 11. An agricultural area's hydrological contribution and connectivity to surface waters seemed to be more important for the development of estrogen concentrations in streams than livestock densities in a catchment or the actual loads of slurry applied. Pond water occasionally contained natural estrogens in concentrations up to 8.6 ng L⁻¹ for E2α. The environmental quality standards of the European Union (0.4 ng L⁻¹ for E2β and 3.6 ng L⁻¹ for E1) were never exceeded for longer than a day in tributaries, but E1 reached critical concentrations for aquatic organisms in ponds.