Naproxen (NPX) is one of common non-prescription non-steroidal anti-inflammatory drugs (NSAIDs) which is widely detected in aquatic environments worldwide due to its high usage and low degradation. NPX exerts anti-inflammatory and analgesic pharmacological effects through the inhibition of prostaglandin-endoperoxide synthase (PTGS), also known as cyclooxygenase (COX). Given its evolutionarily relatively conserved biological functions, the potential toxic effects of NPX on non-target aquatic organisms deserve more attention. However, the ecotoxicological studies of NPX mainly focused on its acute toxic effects under higher concentrations while the chronic toxic effects under realistic concentrations exposure, especially for the underlying molecular mechanisms still remain unclear. In the present study, Daphnia magna, being widely distributed in freshwater aquatic environments, was selected to investigate the toxic effects of environmentally relevant concentrations of NPX via determining the response of the Nrf2/Keap1 signaling pathway-mediated antioxidant system in acute exposure, as well as the changes in life-history traits, such as growth, reproduction, and behavior in chronic exposure. The results showed that the short-term exposure to NPX (24 h and 48 h) suppressed ptgs2 expression while activating Nrf2/Keap1 signaling pathway and its downstream antioxidant genes (ho-1, sod, cat and trxr). However, with prolonged exposure to 96 h, the opposite performance was observed, the accumulation of malondialdehyde (MDA) indicated that D. magna suffered from severe oxidative stress. To maintain homeostasis, the exposed organism may trigger ferroptosis and apoptosis processes with the help of Silent mating type information regulation 2 homologs (SIRTs). The long-term chronic exposure to NPX (21 days) caused toxic effects on D. magna at the individual and population levels, including growth, reproduction and behavior, which may be closely related to the oxidative stress induced by the drug. The present study suggested that more attention should be paid to the ecological risk assessment of NSAIDs including NPX on aquatic non-target organisms.