Carbon dots (CDs) exhibit a wide range of desirable properties including excellent photoluminescence, photostability, and water solubility, making them ideally suitable for use in the context of drug delivery, bioimaging, and related biomedical applications. Before these CDs can be translated for use in humans, however, further research regarding their in vivo toxicity is required. Owing to their low cost, rapid growth, and significant homology to humans, zebrafish (Danio rerio) are commonly employed as in vivo model systems in the toxicity studies of nanomaterials. In the present report, our group employed a hydrothermal approach to synthesize CDs and then assessed their toxicity in zebrafish. The resultant CDs were roughly 2.4 nm spheroid particles that emitted strong blue fluorescence in response to the excitation at 365 nm. These CDs did not induce any evident embryonic toxicity or did cause any apparent teratogenic effects during hatching or development when dosed at 150 μg/mL. However, significant effects were observed in zebrafish embryos at CD concentrations >200 μg/mL, including pericardial and yolk sac edema, delayed growth, spinal cord flexure, and death. These high CD concentrations were further associated with the reduction in zebrafish larval locomotor activity and decreased dopamine levels, reduced frequencies of tyrosine hydroxylase-positive dopaminergic neurons, and multiple organ damage. Further studies will be required to fully understand the mechanistic basis for CD-mediated neurotoxicity, with such studies being essential to fully understand the translational potential of these unique nanomaterials.