Among aquatic organisms, filter feeders are particularly exposed to the ingestion of microplastics (MPs) and nanoplastics (NPs). The present study investigates the effect of environmental microplastics (ENV MPs) and nanoplastics (ENV NPs) generated from macro-sized plastic debris collected in the Garonne River (France), and polystyrene NPs (PS NPs) on the freshwater bivalve Corbicula fluminea. Organisms were exposed to plastic particles at three concentrations: 0.008, 10, and 100 μg L−1 for 21 days. Gene expression measurements were conducted in gills and visceral mass at 7 and 21 days to assess the effects of plastic particles on different functions. Our results revealed: (i) an up-regulation of genes, mainly involved in endocytosis, oxidative stress, immunity, apoptosis, and neurotoxicity, at 7 days of exposure for almost all environmental plastic particles and at 21 days of exposure for PS NPs in the gills, (ii) PS NPs at the three concentrations tested and ENV MPs at 0.008 μg L−1 induced strong down-regulation of genes involved in detoxication, oxidative stress, immunity, apoptosis, and neurotoxicity at 7 days of exposure in the visceral mass whereas ENV MPs at 10 and 100 μg L−1 and all ENV NPs induced less pronounced effects, (iii) overall, PS NPs and ENV MPs 0.008 μg L−1 did not trigger the same effects as ENV MPs 10 and 100 μg L−1 and all ENV NPs, either in the gills or the visceral mass at 7 and 21 days of exposure. This study highlighted the need to use MPs and NPs sampled in the environment for future studies as their properties induce different effects at the molecular level to living organisms.