This study investigates the effects of iron oxide (Fe₃O₄) and aluminum (Al) nanoparticles on the reproductive cells and embryonic development of common carp (Cyprinus carpio), a key species in global aquaculture. Given the growing application of nanomaterials across industries and their increasing presence in aquatic ecosystems, understanding their impact on fish reproduction and development is critical. The study was conducted in two parts: first, reproductive cells (sperm and eggs) were exposed to varying concentrations (0.0001–0.05 g) of Fe₃O₄ and Al nanoparticles during artificial fertilization. Results indicated that low concentrations (0.0001 g and 0.001 g) of both nanoparticle types enhanced fertilization rates, while higher concentrations significantly reduced embryo viability and increased mortality. In the second part, common carp were fed diets supplemented with Fe₃O₄ nanoparticles (10 mg and 100 mg per 10 g feed) for 7 days. Histological and ultrastructural analyses of the intestinal tissue revealed dose-dependent cytotoxic effects, including microvilli degradation, mitochondrial damage, and nanoparticle accumulation in epithelial and vascular cells. These findings highlight the dualistic nature of nanoparticle exposure—potentially beneficial at low doses but harmful at higher concentrations—underscoring the need for regulated nanoparticle usage in aquaculture. The results provide valuable insights for establishing safe biotechnical standards in fish farming under ecologically sustainable conditions.