This study aimed to determine toxic element concentrations in aquatic environments, including water and sediment, and in the Hampala macrolepidota fish, and to evaluate chromosome abnormalities, serum liver enzyme changes and liver histopathological alterations in H. macrolepidota from the Nam Kok River near the Sepon gold–copper mine, Lao People’s Democratic Republic, as compared with a control area without mining activity. The results revealed significant differences (p < 0.05) in As, Ba, Cu, Fe, Mn, Ni, Se and Zn in water, in all of the studied potentially toxic elements in sediment, and in As, Ba, Cd, Cr, Cu, Mn, Ni, Se, and Zn in the fish between the study and control areas. A chromosome assessment demonstrated 6 types of chromosome abnormalities, among which centric gap had the highest total number of chromosome abnormalities. Percentage of chromosome abnormalities, percentage of cells with chromosome abnormalities and serum liver enzymes in H. macrolepidota were significantly different (p < 0.05) between the two studied areas and were higher in the contaminated fish than in the control fish. The observation of liver histopathological changes revealed cellular degeneration, such as nuclear damage, abnormal cytoplasmic mitochondria and the disintegration of rough endoplasmic reticulum. The results indicate that the contamination of potentially toxic elements in the Nam Kok River near the Sepon gold–copper mine area negatively affected chromosomes, serum liver enzymes and liver cell structures in H. macrolepidota.