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This study represents the first report comparing the acute toxicity of three types of nanoplastics (polystyrene (PS), polypropylene (PP), and polyethylene (PE)) on multiple biological endpoints of Artemia franciscananauplii, a commonly used model organism in ecotoxicology. The nauplii were exposed to four concentrations (0.05, 0.5, 5, and 50 mg L−1) of each nanoplastic type for a duration of 48 h. The study assessed their mortality, growth, morphological changes, bioaccumulation, oxidative stress, apoptosis, histopathology, and gene expression. Among the nanoplastic types tested, PS-NPs exhibited the highest toxicity, followed by PE-NPs and PP-NPs. Exposure to high concentrations of PS-NPs (>5 mg L−1) resulted in high mortality rates, impaired growth, delayed developmental stages, and extensive histopathological damage in the nauplii. Furthermore, the expression of several genes associated with molting, protein folding, energy metabolism, and apoptosis in the nauplii was modulated by exposure to PS-NPs at 5 mg L−1concentration. Moreover, the highest bioaccumulation in the gut and other organs of the nauplii was observed for PS-NPs across all exposure concentrations. Oxidative stress and apoptosis were induced by all types of nanoplastics at all exposure concentrations. The findings of this study highlight the potential consequences of nanoplastic pollution on aquatic ecosystems. It underscores the need for further research to explicate the mechanisms and chronic impacts of nanoplastic toxicity on aquatic organisms.