Estuaries are heavily impacted by pollutants from different sources such as urban sewage, industrial waste and agricultural runoff. Endocrine-disrupting chemicals (EDCs) are very concerning pollutants to estuarine wildlife, but little is known about their impact on microscopic biota such as zooplankton. The aim of this work was to investigate the effects of a model EDC, the 17α-ethinylestradiol (EE2), on two copepod species inhabiting the Basque coast (Southeastern Bay of Biscay) estuaries:Acartia clausi(autochthonous neritic species) andAcartia tonsa(non-indigenous brackish species). Female copepods were collected at population maximum time (spring forA. clausiand summer forA. tonsa) and exposed individually to 5 ng/L (low), 5 µg/L (medium) and 500 µg/L EE2 (high) doses, from environmental concentrations found in sewage effluents to toxicological concentrations. After 24 h exposure, the survival rate of experimental individuals was checked and the lethal concentration LC50 was calculated. The number of egg-producing females and the amount of egg laying and egg hatching were recorded. The integrated biomarker index (IBR) was calculated to integrate the overall effects of EE2 exposure. Both species had reduced survival rates at 500 µg/L, and the LC50 was lower inA. tonsa(158 µg/L) compared toA. clausi(398 µg/L). The number of eggs laid was significantly reduced inA. clausiat EE2 medium and high doses, while a reduction in the number of eggs inA. tonsawas observed only at the high dose. However, no significant differences were detected in the egg hatching success of exposedA. clausiandA. tonsa. IBR index showed that EE2 had the most detrimental effects onA. tonsaandA. clausifemales at the 500 µg/L dose. In conclusion, after 24 h of exposure, EE2 reduced female copepod survival and disrupted reproductive output, but only at high non-environmentally relevant concentrations.