The bottom sediment of reservoirs has many functions. Among them, matter sorption is a very important one, and results in many side-effects on the reservoir sediment forming the water–bottom sediment system. As a result, bottom sediment can also be an indicator of anthropogenic water pollution. There is only very little knowledge of this situation in the study area. The main objective was the analysis of heavy metal accumulation in bottom sediment, as well as their ability to migrate throughout the water–bottom sediment system and their spatial distribution in the Kapshagay Reservoir in Kazakhstan. Heavy metal concentrations, in the both water samples and the bottom sediment, were determined using the atomic absorption spectrophotometric method. Surfer software was used to visualize the processes of migration and accumulation. Another objective was the development of model maps of the spatial distribution of metals in the reservoir water area, which indicated significant anthropogenic loads. It is obvious that both the transboundary inflow of the Ili River and the inflow from small rivers in the territory of Kazakhstan are the reasons for the anthropogenic water and sediment load. The results of the spectrometric analysis verify the water pollution in the reservoir, revealing increased concentrations of zinc reaching up to 10.8 µg/L and lead up to 32.7 µg/L, transported by the transboundary runoff of the Ili River and by the small rivers on the left bank into the Kapshagay Reservoir. Sediment concentrations close to the central part and dam zone of the reservoir reached the following values: zinc up to 37.0 mg/kg and lead up to 8.8 mg/kg. The results of this study indicate a significant anthropogenic load of the ecological conditions of the Kapshagay Reservoir. This is discussed and compared with other relevant studies.

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