Geochemical and mineralogical analysis of the bottom sediment cores of small lakes can be used as the basis for radio-ecological monitoring and environmental protection measures. Here, features of the radionuclide activity distribution in components of the limnetic ecosystems of the central Baraba lowland were studied, and factors affecting radiocesium absence in the bottom sediment of Lake Sarbalyk were identified. Fieldwork included the sampling of limnetic ecosystem components, bottom sediment weighing, and the determination of pH, Eh, TDS and oxygen content. Subsequent laboratory investigation involved the determination of major and trace element concentrations by atomic absorption spectrometry and X-ray fluorescence analysis; mineral composition by X-ray diffractometry (XRD); analysis of sample morphology and composition via scanning electron microscopy; and natural radionuclide and radiocesium content determination by the gamma-spectrometric method. Radiocesium is present in all the studied lake bottom sediments of the central Baraba lowland in the upper horizons, with the exception of Lake Sarbalyk. Limnetic ecosystem components were analyzed using modern analytical methods, considering the distribution features of natural and artificial radionuclides in catchment area soils, tussocks and the bottom sediment of Lake Sarbalyk. The results revealed that the absence of radiocesium in the bottom sediment of Lake Sarbalyk is due to two factors: the characteristics of the lake overgrowth and the sorption of dissolved forms of Cs-137.