Multifunctional nanoparticles (NPs) represent exciting prospects for a myriad of in vivo applications, such as targeted drug delivery and medical diagnostics. For these applications to be viable in the clinic, it is essential that NPs are biocompatible, with negligible toxicity. The use of zebra fish as a model to evaluate NP biocompatibility is growing rapidly. This chapter details a range of different methods for the assessment of NP toxicity using both embryonic and adult zebra fish, including teratogenicity, mortality, effects on hatching, reproduction and behavioral responses, immunotoxicity, and genotoxicity, augmented by in vivo imaging. This is supplemented with specific examples of biocompatibility testing in zebra fish of metal-, metal-oxide-, and carbon-based NPs, including graphene quantum dots. This information will help to inform future studies that aim to develop biocompatible NPs as drug carriers and imaging agents for therapeutic and diagnostic applications.