In the present conditions of urbanization of the world, fresh water becomes a scarce natural resource. It is known that the vast reserves of fresh water are concentrated in glaciers. In Russia, the majority of glaciers are concentrated in the Arctic, as well as in high-altitude areas of Kamchatka, Altai and the Caucasus. Trace elements are global priority pollutants, monitoring which is an actual problem. Particularly acute problem of water quality, in terms of trace elements, gains in mining and glacial highlands of the Caucasus, where rivers feeding the flat part of the Kabardino-Balkarian Republic originate. Formation of trace-element composition of mountainous glacial river waters occur naturally, by their transferring with the precipitation, from the soil, by wind transfer, but mainly due to the metallogenic features of water-bearing rocks and their ore specialization, and as studies have shown different in various altitudinal zones. It is known that the trace element composition of mountainous catchments of the Caucasus differs by a high concentration of many trace elements, which is caused by the spread of ore-bearing rocks in their basins. The results of the study of trace elements Mn, Mo, Ni, Cr, Pb, Cd in the waters of the glacial river Cherek-Balkarsky are given in the article. It is established that the pollution of river waters by trace elements in the upper reaches is natural geochemical and geomorphological background, due to leaching from rocks. It is noted that at the exit of the river to the plain the concentration of trace elements (except lead) decreases significantly and their number is much lower than in the upper reaches. The article also presents the minimum, maximum, and average concentrations of major ions and nitrogen-containing substances in the waters of the river Cherek-Balkarsky in the period of winter low water. According to that exceedance of the MAC was twice observed (p. 6.- R. Cherek, 110 km), namely nitrite and ammonium ions in 1,87 times and 6.4 times respectively, due to the pollution of the lower reaches of the river Cherek by the waste from the populated areas – runoff from residential complexes and farms.