Presently, nanoparticles (NPs) technology is a booming business marked by a significantly fast growth rate that covers a wide range of industries. NPs demand increases and they have a potential market value. The nanotoxicity sector has grown significantly for the last 10-15 years, which will pose serious problems in the coming future. Nano-toxicology is an innovative area of toxicological study that assesses the toxicological assets of NPs to decide whether they constitute a risk or an ecological problem and to what degree. To assess the different NPs toxicity, numerous nanotoxicological studies were piloted using different methods. The vital mechanisms of nanomaterial toxicity were recently studied especially in aquatic wildlife. In recent years, nanoparticle toxicity evaluation amplified exponentially by using zebrafish as an animal prototypical system. Zebrafish has been tested as an established model system for experimental biological study and are evolving as a solid nanotoxicity prototype which is progressively used as an in vivo model. It is principally used as a platform for rapid testing and assortment of molecules in the object or phenotype techniques. It offers a number of advantages over other living prototypes by offering prospects to speedily screen nanoparticulate medicines beneath in-vivo environments, also an economical way to link the present gap among in vitro and vertebrate studies. Many researchers have summarized experimental parameters critically used by zebrafish as an animal model for biomedical tests such as sample size, organ and type wild against transgenic lines. Current chapter will discuss considerable factors of experimentation, advantages and usage of zebrafish in nanomedicine; different methods of evaluating the nanotoxicity such as hatching exploration; malformation of embryos and organs of development; genetically modified zebrafish by means of living biosensor; disturbance in the endocrine system, skin and gill; reproductive toxicity; genotoxicity; neurotoxicity; immune-toxicity; and behavioral analysis. Furthermore, it will also discuss an overview of studies about investigation of the toxicity of silver, carbon nanotube, metal oxide and quantum dots nanoparticles using zebrafish. At the end, future lookouts of zebrafish model are discussed. It is projected that this chapter will update study directed at emerging biocompatible nanoparticulates for a choice of uses and toxicity investigation.