To evaluate the use of morphological abnormalities for standard testing of endocrine‐disrupting substances (EDS), we tested the hypothesis that developmental abnormalities are a sensitive indicator of exposure to waterborne estrogenic and antiestrogenic EDS during embryonic, larval, and juvenile stages in the common estuarine killifish, the mummichog (Pisces: Cyprino‐dontidae). Static exposures with daily renewal were carried out with 10 to 10,000 ng/L of the estrogen agonist 17α‐ethynylestradiol (EE2) or antagonist ZM189,154 (ZM) for the first 25 or 60 d of life. Incidence of skeletal abnormalities (scoliosis, lordosis, head, craniofacial, jaw, fin) and soft tissue abnormality (anal swelling) were significantly increased by EE2 but only at high concentrations (1,000 or 10,000 ng/L). Sixty‐day exposure produced more severe abnormalities than 25‐d exposure and in a higher proportion of fish. Within the longer exposure, 10,000 ng/L EE2 produced more abnormal fish than 1,000 ng/L (100% vs 51.6%) and more abnormalities per abnormal fish (5.73 vs 1.47). Fish reared to 12 months in clean water after exposure for 60 d to 10,000 ng/L EE2 survived at a lower rate than controls, retained abnormalities with the exception of anal swelling and, like fish exposed to other concentrations of EE2 and ZM, showed increased weight at length at 6 and 12 months. Sixty‐day exposure to ZM increased the incidence of scoliosis (1,000 ng/L) but decreased the overall incidences of abnormal fish and lordosis (10 and 10,000 ng/L). No impacts of EE2 or ZM were observed before hatch, and clearing and staining of larvae demonstrated that expression of vertebral abnormalities coincided temporally with ossification. We conclude that morphological abnormalities in mummichogs are not a sensitive indicator of exposure to estrogenic or antiestrogenic waterborne EDSs at environmentally relevant concentrations.