High mountain areas provide water resources for a large share of the world’s population. The ongoing deglaciation of these areas is resulting in great instability of mountainous headwater regions, which could significantly affect water supply and intensify dangerous hydrological processes.

The hydrological processes in mountains are still poorly understood due to the complexity of the natural conditions, great spatial variation and a lack of observation. A knowledge of flow-forming processes in alpine areas is essential to predict future possible trends in hydrological conditions and to calculate river runoff characteristics. The goal of this study is to gain detailed field data on various components of natural hydrological processes in the alpine areas of the North Caucasus and Central Tien Shan, and to investigate the possibility that the isotopic method can reveal important regularities of river flow formation in these regions. The study is based on field observations in representative alpine river basins in the North Caucasus (the Dzhankuat river basin) and the Central Tien Shan (the Chon-Kyzyl-Suu river basin) during 2013–2015. A mixing-model approach was used to conduct river hydrograph separation. Isotope methods were used to estimate the contribution of different nourishment sources in total runoff and its regime. d¹⁸О, dD and mineralization were used as indicators. Two equation systems for the study sites were derived: in terms of water routing and runoff genesis. The Dzhankuat and Chon-Kyzyl-Suu river hydrographs were separated into 4 components: liquid precipitation/meltwaters, surface routed/subsurface routed waters.