Mussels are highly efficient filter feeders, playing a crucial role in managing eutrophication and assessing pollution. Although research on nanoplastic (NP) toxicity in marine organisms is expanding, studies on freshwater species remain limited despite freshwater ecosystems being disproportionately biodiverse and vulnerable to pollutants. Here, we quantified the effects of polystyrene nanoplastics (PS-NPs, 50 nm) at concentrations of 0, 2, 20, and 200 μg/L on different growth stages of the freshwater mussel Cristaria plicata. After a 45-day exposure, PS-NPs at concentrations ≥ 20 μg/L damaged intestinal epithelial cilia in both age groups. Exposure to 200 μg/L PS-NPs significantly increased malondialdehyde levels and decreased superoxide dismutase activity in both groups, with adults showing a significant rise in total protein content and juveniles exhibiting marked increases in respiratory and ammonia excretion rates. Additionally, PS-NP exposure significantly altered the relative abundance of gut microbial phyla, including Proteobacteria, Firmicutes, Verrucomicrobiota, and Bacteroidota, with Fusobacteriota also being affected in adults. Juveniles were more sensitive to physiological changes, whereas adults exhibited greater microbiota shifts in response to PS-NP exposure. Therefore, this study provides new insights into the stage-specific effects of PS-NPs on intestinal integrity and physiological and biochemical health in freshwater mussels, underscoring the need for targeted management strategies to protect freshwater ecosystems.