The aims of present work were to analyze on the base of our data of 1997-2017 the changes in the content of heavy metals in 118 water bodies in Kazakhstan, determine the relationship between the content of heavy metals and the level of anthropogenic load, to reveal natural factors affecting the accumulation of heavy metals in the water. It was revealed that average Cd content was 0.01-7.7 μg dm-3 , Cu-1.6-158.2, Zn-1.5-44.1, Pb-1.4-19.4, Cr-0.05-14.6, Ni-0.2-227.2 μg dm-3. The level of toxic pollution of water bodies increased against the altitude gradient. The relationship between the content of heavy metals and the altitude of location of a water body was indirect, because was an accompanying change in the pH, temperature, and TDS of water. In water bodies with a TDS above 2000 mg dm-3, Pb, Cr, Cd and Cu were accumulating most intensively, whereas fresh waters contained higher amounts of Zn and Ni. Regression analysis revealed the leading role of pH in the accumulation of heavy metals in water bodies. An increase in anthropogenic load in the direction from mountainous areas to plains led to the additional enrichment of water bodies with heavy metals.