Mercury (Hg), cadmium (Cd) and lead (Pb) are toxic metals that continue to attract much attention because they are prone to be accumulated in fish tissues and can harm human health if taken up with food. Data acquired by studying the bioaccumulation of these metals in the various fish species from water bodies along a latitudinal gradient in Russia (from northern Arctic lakes to the southern mouth segments of the Volga River) are utilized to identify general tendencies and specifics in the accumulation of toxic metals depending on the aquatic environment and temperature. Results demonstrate that small quantities of the metals are accumulated in various functionally important organs: Hg is enriched in the liver and muscles, Cd in the kidneys and gills, and Pb in the kidneys and liver. The metals are proved to be simultaneously accumulated in all organs and tissues of the organism, and this reflects the uptake of the metals by the organism and their subsequent distribution in it. The aquatic environment and fish habitats affect the elements’ bioavailability. The metals are more significantly accumulated in predatory fish. At low Hg concentrations in the water, statistically significant dependences were identified between Hg accumulated in predatory fish organisms and concentrations of organic matter in the water. Cd is more bioavailable in waters with low pH. Pb displays the strongest dependence of its bioaccumulation in low-salinity water. Extensive data on fish in water bodies occurring in large territories in Russia, from the Arctic to warm southern latitudes, indicate that climate affects the intensity of Hg accumulation, whereas the accumulation of the other metals also depends on the Ca concentrations, with the uptake of these metals being more significant at low Ca concentrations. Concentrations of toxic metals in the muscles of the fish were below the values critical to food to be consumed by humans.