SiO2 nanoparticles (SNPs), which reportedly have low potential side effects, are used in various applications, for example, as food additives, for drug delivery, and as semiconductors, but these NPs are a growing concern because a few studies have shown potential risks to human health, such as fatty liver formation. In recent years, dietary habits have changed, and more refined foods, sugary beverages, and fast food are being increasingly consumed during daily life; therefore, the dietary habits have changed toward increasing consumption of high-fat diets, which may increase the incidence of liver and kidney disease. Our in vivo study demonstrated that the administration of SNPs in drinking water in combination with a high-fat diet was associated with the accumulation of SNPs and triglycerides in renal tissue; elevations in the blood urea nitrogen, uric acid, and creatinine levels in serum; the formation of Basophilia and tubular cell sloughing; abnormal renal parenchyma, cysts, and hyaline casts; the induction of proliferating cell nuclear antigen and markers for chronic kidney disease such as vimentin, lipocalin 2, kidney injury molecule; the activation of fibrosis and inflammation; increased oxidative stress; and the development of chronic kidney disease. The evidence showed that long-term treatment of SNPs in drinking water might induce renal injury in individuals with modern dietary habits and provided important results for evaluating the safety of SNPs, especially for human health.