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Silicon oxide (SiO2) nanostructures (SiO2NS) are increasingly being incorporated into an array of products, notably in the food, pharmaceutical, medical industries and in water treatment systems. Amorphous SiO2NS have low toxicity, however, due to their great versatility, superficial modifications can be made and these altered structures require toxicological investigation. In this study, SiO2NS were synthetized and amine-functionalized with the molecules (3-aminopropyl)triethoxysilane (APTMS) and 3-[2-(2-aminoethylamino)ethylamino]propyltrimethoxysilane (AEAEAPTMS), named SiO2NS@1 and SiO2NS@3, respectively. The bare SiO2NS, SiO2NS@1 and SiO2NS@3 samples were characterized and the influence of the culture medium used in the toxicological assays was also evaluated. The effect of amine functionalization of SiO2NS was investigated through acute and chronic toxicity assays with Daphnia magna. Modifications to ultrastructures of the intestine and eggs of these organisms were observed in TEM and SEM analysis. The toxicity was influenced by the surface modifications and a possible Trojan horse effect was highlighted, particularly in the case of chronic exposure. Exposure to all NSs promoted alterations in the microvilli and mitochondria of the D. magna intestine and some damage to egg cells was also observed. The results demonstrate the importance of carrying out a full characterization of these materials, since surface modifications can enhance their toxic potential.