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Zinc oxide nanoparticles (ZnO NPs) pose a major threat to aquatic life and their presence in the aquatic environment requires attention. This study intends to examine the impacts of ZnO NPs on Brachidontes pharaonis. Brachidontes pharaonis were divided into four groups, the control group and experimental groups exposed to ZnO NPs at concentrations of 1 mg/L, 5 mg/L, and 8 mg/L. The results revealed a decrease in protein and glucose, along with an increase in cholesterol, HDL, LDL, and triglycerides. The SDS-PAGE showed changes in the concentration of protein. In histological observations, there was necrosis in the epithelial cells, infiltration in the connective tissue between ovarian follicles, hemorrhage of blood vessels in gill filaments, and fibrosis in muscle myofibrils. Histochemical studies showed a rise in mucous cells in gill filaments and an increase in collagen fibers in the muscle. As concluded, ZnO NPs lead to alteration in biochemical parameters, protein profile, and histopathological changes in B. pharaonis.