Endocrine disruptors are chemicals that have been in the spotlight for some time now. Their modulating action on endocrine signaling pathways made them a particularly interesting topic of research within the field of ecotoxicology. Traditionally, endocrine disrupting properties are studied using exposure to suspected chemicals. In recent years, a major breakthrough in biology has been the advent of targeted gene editing tools to directly assess the function of specific genes. Among these, the CRISPR/Cas9 method has accelerated progress across many disciplines in biology. This versatile tool allows to address antagonism differently, by directly inactivating the receptors targeted by endocrine disruptors. Here, we used the CRISPR/Cas9 method to knock out the different estrogen receptors in zebrafish and we assessed the potential effects this generates during development. We used a panel of biological tests generally used in zebrafish larvae to investigate exposure to compounds deemed as endocrine disrupting chemicals. We demonstrate that the absence of individual functional estrogen receptors (Esr1, Esr2b, or Gper1) does affect behavior, heart rate and overall development. Each mutant line was viable and could be grown to adulthood, the larvae tended to be morphologically grossly normal. A substantial fraction (70%) of the esr1 mutants presented severe craniofacial deformations, while the remaining 30% of esr1 mutants also had changes in behavior. esr2b mutants had significantly increased heart rate and significant impacts on craniofacial morphometrics. Finally, mutation of gper1 affected behavior, decreased standard length, and decreased bone mineralization as assessed in the opercle. Although the exact molecular mechanisms underlying these effects will require further investigations in the future, we added a new concept and new tools to explore and better understand the actions of the large group of endocrine disrupting chemicals found in our environment.