Because they are widely used, copper oxide nanoparticles (CuO NPs) are likely to enter the aquatic environment and then reach the sediment. We have examined the effect of CuO NPs in the freshwater endobenthic bivalve Corbicula fluminea. Some previous studies have investigated effects at biochemical and physiological levels, but molecular endpoints are still poorly studied despite they are sensitive in early detection of NPs effect. In the present study, we have investigated short-term effects (96 h) of CuO NP (12, 30 nm; 0, 20 and 100 μg/L) using molecular endpoints as well as more conventional biochemical and physiological markers. The expression of antioxidant (CuZnSOD, MnSOD, Cat, Se-GPx, Trxr) and antitoxic (GST-Pi, HSP70, MT, Pgp, MRP1) related genes was measured at the mRNA level while antioxidant (SOD, TAC) and antitoxic (GST, ACP) defenses, energetic reserves and metabolism (ETS, Tri, LDH), and cellular damages (LPO) were assessed using a biochemical approach. The filtration rate measured at 96 h provided information at the physiological scale. Gene expression and filtration rate were responsive to CuO NPs but the effects differed according to the NP size. The results suggest that defense mechanisms may have been set up following 30 nm-NP exposure. The response to 12 nm-NP was lower but still showed that exposure to 12 nm-NP led to activation of cellular elimination mechanisms. The lowering of the filtration rate may have protected the organisms from the contamination. However, this raised the question of further repercussions on organism biology. Together, the results (i) indicate that CuO NP may exert effects at different levels even after a short-term exposure and (ii) point out the precocity of molecular response.