The results of chemical and isotopic analyses of waters of the Transboundary Zeravshan River, the Vakhsh River and its tributaries are presented. As an impact indicator of the mining enterprise wasterwater in the basin of the Zeravshan River on the quality of water a differential method of changing of the chemical composition of water before and after the tailing dams wasterwater is applied. The change of isotopic composition of the Zeravshan River and its tributaries from upstream to downstream is detected. The exchange of groundwater and surface waters in Muksu River Basin by isotopic methods is observed