The determination of potentially toxic element concentrations in fish is an important topic from the point of view of both nature conservation and human consumption. The aim of this study was to assess the concentrations of S, K, Ca, Cr, Mn, Fe, Zn, Rb, Sr, Mo, and P in benthic and pelagic fish species in the Karatal river, which is fed by melting glaciers from the Dzungarian Alatau in Kazakhstan. In September 2022, 48 fish samples were collected. It has been demonstrated that the accumulation of chemical elements in fish species can be explained by both the physiological parameters of the fish species and the influence of glaciers that feed river habitats. The data presented in this study provide a synergistic view of pollutants affecting fish populations. Benthic fish contained more manganese and strontium than pelagic species, while the mutual accumulation of potassium, chromium, rubidium, and molybdenum was higher in pelagic fish. The synergistic concentration of calcium and phosphorus in pelagic fish was higher than that in benthic species, while the amount of zinc and sulfur was higher in benthic animals. Relatively elevated levels of mercury in fish were found. The study contributes to the discussion about the role of glacial environments in loading pollutants to aquatic systems.