Growing experimental data on the adverse effects of microplastic pollution on marine biota indicate that the size of the plastic particles is a key determinant of toxicity. Particulalarly, despite the high bioavailability and potentially extensive presence of nanoplastics in aquatic environments, the biological fate of nanoplastics is largely unknown because of analytical limitations in detection and quantification. Here, we investigated size-dependent toxicity at different levels of biological organizations in the marine organisms, from bioaccumulation as an initiating event to adverse in-vivo outcomes. Nanoplastics strongly retarded the reproduction and population growth of marine zooplanktons, while microplastics were associated with moderate effects. We demonstrated a stronger accumulation of nano-sized microbeads in the marine organisms compared to micro-sized ones, which was associated with oxidative stress-induced damages, as revealed by biochemical and transcriptomic analysis. Furthermore, in addition to the digestive organs (e.g., the gut and intestines) of the fish that are constantly exposed to the water column via ingestion, nanoplastics were shown to selectively bioaccumulate in the gills and ovary, implying a unique mode of action of bioaccumulation, as revealed by a stable carbon isotopic approach. Our study provides a better insight into toxicity of micro- and nanoplastics and their biological fate in the marine organisms.