Clean and safe water is fundamental for human and environmental health. Traditional remediation of textile dye-polluted water with chemical, physical, and biological processes has many disadvantages. Due to this, nano-engineered materials are drawing more attention to this area. However, the widespread use of nano-particles for this purpose may lead to photocatalytic degradation of xenobiotics, while increasing the risk of nano-particle-induced ecotoxicity. Therefore, we comparatively evaluated the toxicity of novel synthesized core@shell TiO2 and SiO2 nano-particles to embryonic stages of Danio rerio and Xenopus laevis. The ability of photocatalytic destruction of the synthesized nano-particles was tested using toxic azo dye, disperse red 65, and the effects of reducing the toxicity were evaluated. The reflux process was used to synthesize catalysts in the study. The samples were characterized by scanning electron microscopy, X-ray fluorescence spectroscopy, X-ray diffractometry, BET surface area, and UV-vis-diffuse reflectance spectra. It was determined that the synthesized nano-particles had no significant toxic effect on D. rerio and X. laevis embryos. On the other hand, photocatalytic degradation of the dye significantly reduced lethal effects on embryonic stages of the organisms. Therefore, we suggest that specific nano-particles may be useful for water remediation to prevent human health and environmental impact. However, further risk assessment should be conducted for the ecotoxicological risks of nano-particles spilled in aquatic environments and the relationship of photocatalytic interaction with nano-particles and xenobiotics.