The research is devoted to the exploration of heavy metal (HM) accumulation in hydrobionts of Lake Markakol, located in Eastern Kazakhstan. The objective of the research was to evaluate the levels of HMs accumulation in aquatic sections, food organisms and fishes, as well as to determine their impact on the ecosystem and potential risks to human health. The study analyzed concentrations of copper, zinc, lead, cadmium, nickel and cobalt in macrophytes, zooplankton, macrozoobenthos and fish tissues (uskuch, Brachymystax lenok). The results show significant exceedances of the maximum permissible concentrations (MPC) for all tested metals, especially in food organisms and fish. The highest concentrations were recorded in liver, gills and muscles, with nickel content reaching 55.6 mg kg-1, and cobalt – 111 mg kg-1, which exceeds MPC by tens and hundreds of times, which indicates a high pollution degree of the aquatic ecosystem. It was established that heavy metals actively migrate along trophic chains, accumulating in hydrobionts tissues, which results in a risk to human health when consuming fish. The obtained data emphasize the necessi