The presence of small-sized plastic particles in marine and freshwater environments is a global problem but their long-term impact on ecosystems and human health is still far from being understood. Nanoplastics (<1000 nm) could pose a real and uncontrolled ecological challenge due to their smaller size and sharp ability to penetrate living organisms at any trophic level. Few studies evaluate the impact of nanoplastics in vivo on the immune system of aquatic organisms, while most of them assessed the impact on indirect markers of immune response such as regulation of gene expression, ROS production or DNA genotoxicity, among others. Moreover, the study of the effects of nanoplastics on aquatic vertebrate species in vivo is still scarce. In this context, we seek to shed light on the underlying effects of polystyrene nanoplastics (PS-NPs) on the immune response in a model fish species (Danio rerio, zebrafish) after an acute exposure, with a combination of in vitro and in vivo experiments. Our results show that PS-NPs (65 nm) are efficiently taken up by zebrafish liver cells, accumulating mainly in lysosomes. Furthermore, the expression of immune genes presents a synergy when cells were simultaneously exposed to PS-NPs, at a low dose and early time point (12 h) and challenged with a viral stimulus (poly(I:C)). Moreover, zebrafish larvae also internalize PS-NPs, accumulating them in the gut and pancreas. However, at concentrations of up to 50 mg l−1 in an acute exposure (48 h), PS-NPs do not interfere with the survival of the larvae after a lethal bacterial challenge (Aeromonas hydrophila). This study addresses the relevant environmental question of whether a living organism exposed to PS-NPs can cope with a real immune threat. We show that, although PS-NPs can induce an immune response, the survival of zebrafish larvae challenged with a bacterial infection after an acute exposure to PS-NP is not decimated with respect to unexposed larvae.