Chronic kidney disease (CKD) is a global public health issue linked to toxic elements like cadmium (Cd) and mercury (Hg), which harm the kidneys even at low exposure levels. Copper (Cu) and zinc (Zn) imbalances could exacerbate inflammation, oxidative stress, and kidney damage because the Cu/Zn ratio could be a critical marker of renal dysfunction. The study evaluated 914 adolescents aged 11–18 through urine samples to assess the presence of kidney damage biomarkers (OPN, KIM-1, CLU, NGAL, and Cys-C) by using Luminex Magpix and trace metals (Cd, Hg, Cu, Zn) by using ICP-mass. Overweight (18.71%) and obesity (12.58%) rates were noted. Cd and Cu showed positive correlations with kidney damage biomarkers, while Zn exhibited protective effects. Regression models indicated that Cd exposure increased kidney damage markers, emphasizing the importance of Cu/Zn ratio. Environmental exposure to Cd affects kidney health even at low levels, as the Cu/Zn ratio correlates with kidney damage markers in low-Cd exposure, suggesting that the Cu/Zn ratio could participate in the nephrotoxicity process, highlighting trace element imbalance as a potential predictor of kidney function decline.