The paper considers the results of long-term studies on some chemical elements’ migration (Al, Fe, Ti, Mn, Cu, Zn, Pb, N, P, Si) in the «bottom sediments – water» system of surface water bodies under the effect of different aquatic environment factors. The greatest effect is made by water bodies’ oxygen regime, pH, and presence of dissolved organic substances, in particular humic substances. The migration of manganese, iron, inorganic nitrogen and phosphorus from bottom sediments is controlled mostly by oxygen regime. Migration of these chemical elements significantly increases, when there is oxygen deficiency and anaerobic conditions are formed in the bottom water layer. It has been observed in both natural and experimental conditions. Man- ganese concentration increases in bottom water in 25–50 times, iron – in 1.3–13, inorganic nitrogen – in 5.3–19.3, and inorganic phosphorus – in 2.8–23 times. The dissolved oxygen concentration hardly has any effect on the migration of aluminium, titanium, copper, zinc, lead, and silicon from bottom sediments into the water. The chemical elements’ migration is significantly affected by a decrease in pH of water contacting with bottom sediments and the presence of humic substances in it. High humic substances concentrations promote a reduction in water pH and oxygen content, which is consumed for their oxidation. A case study of several water bodies illustrates the cumulative effect of water pH lowering, anaerobic conditions at the solid and liquid phases’ interface, as well as complexation with humic substances on chemical elements’ migration from bottom sediments. Experimental modeling has shown that the metal migration from bottom sediments occurs both due to their labile fractions and complex compounds with dissolved organic matter, especially with humic substances of low molecular weight (≤2.0 kDa). The share of the metal labile fraction gets higher, when water pH decreases. Under recent climate change, the probability of water’s secondary pollution with different chemicals increases significantly in summer. This is mainly caused by oxygen deficiency, water pH lowering, and reducing conditions at the «bottom sediments – water» interface with hydrogen sulphide being formed. This is especially true for highly eutrophic water bodies subject to human impact. The aquatic environment toxicity can get considerably higher due to the migration of chemicals with strong toxic properties from bottom sediments, as well as labile metal fractions, marked by higher bioavailability for hydrobionts.