The paper presents the results of radiation surveying and determination of radionuclide and elemental composition in water objects (soil, bottom sediments, water) of the transboundary rivers Shu, Shor-Koo, Aksu, Karabalta, Toktas as well as of Tasotkel water-storage in Kazakhstan in vicinity of the border with Kyrgyzstan. Increased contents of natural radionuclides of 238 U and 232 Th series, As, Co, Cs, Cu, Hf, Mo, Pb, Sb, Sc, Zn, Zr and rare earth elements were observed in soil and bottom sediment samples. Increased contents of the following toxic elements were revealed in water samples: B, As, Mo, Ba, U. Negative influence of radiation-hazardous sites in Kyrgyzstan on the contamination of the transboundary rivers with natural radionuclides and toxic elements was revealed.