Endocrine disrupting chemicals are a threat to natural fish populations in the aquatic environment. Their toxicity is usually discussed relative to concentrations in the water the fish are exposed to. In the case of the synthetic compound 17-alpha-ethynylestradiol (EE2), a common and persistent estrogen, concentrations around 1 ng/L have repeatedly been found to induce toxic effects in fish. Here, we used brown trout (Salmo trutta) from a natural population to study EE2 take up and how it affects early life-history. We collected adults during the spawning season, produced 730 families in vitro (to control for potential maternal and paternal effects on embryo stress tolerance), and singly raised 7,300 embryos (in a 2 mL static system) that were either exposed to one dose of EE2 at 1 ng/L (i.e., 2 pg/embryo) or sham-treated. We found that EE2 concentration did not significantly change over a period of 3 months in control containers without embryos. Embryos took up most of the 2 pg EE2 within about 4 weeks at 4.6°C. EE2 treated embryos experienced higher mortality, delayed hatching of the survivors, and had reduced size at hatching. Our findings suggest that the toxicity of EE2 is often underestimated when discussed at the level of concentrations in water only.