Zebrafish (Danio rerio) have become a powerful model for studying human development and disease. Correspondingly, the use of zebrafish in the field of toxicology has expanded with zebrafish larvae now being routinely used to study phenotypic, cellular, and molecular toxicological outcomes. The number of tools available to study the specific effects of toxicant exposures on development has significantly increased and the application of these techniques allows for the dissection of toxicant effects at the cellular and molecular level. This collection aims to highlight how tools can be utilized in the study of mechanisms of toxicity in zebrafish at different stages of zebrafish development.