Sulfamethoxazole (SMZ), a kind of sulfonamide antibiotic, is widely used in both human and veterinary medicine. Frequent detection of SMZ in natural aquatic environments has prompted growing attention and posed ecological risks to the ecosystem and human health. In this study, we investigated the ecotoxicological properties of SMZ upon Daphnia magna, and the mechanisms of the deleterious effects of SMZ were attempted to be elucidated by investigating a chain of parameters, including survival, reproduction, growth, locomotor behavior, metabolism, as well as levels of related enzyme activity and gene expression. After a 14-d sub-chronic exposure to SMZ at environmentally relevant concentrations, we observed virtually no lethal effect, weak growth inhibition, significant reproductive damage, evident ingestion rate decline, obvious change in locomotor behavior, and remarkable metabolic disorder. Notably, we identified SMZ as an inhibitor against acetylcholinesterase (AChE)/lipase in D. magna both in vivo and in vitro, which explained the adverse effects of SMZ on locomotor ability and lipid metabolism at the molecular levels. Furthermore, the direct interactions between SMZ and AChE/lipase were confirmed by using fluorescence spectrum and molecular docking. Together, our findings provide a new insight to advance the understanding of the environmental effects of SMZ on freshwater organisms.