Climate warming and anthropogenic impact causes transformation of geocryological conditions in the river basins of the North-East of Russia. Changes in the thickness of the active layer, configuration of taliks, types of landscapes and other factors lead to transformation of water exchange processes between surface and groundwater runoff. This is manifested in the seasonal redistribution of the components of the water balance, accelerated melting of aufeis, change in the ratio of waters of different genesis in the structure of river runoff. As a result, natural and anthropogenic risks that affect the safe and efficient development of infrastructure and socio-economic processes are increasing. At the same time the system of observations developed in the Soviet period has been practically destroyed in the region. This paper offers a vision of organizing complex multidisciplinary research to assess and project the changes in the conditions of underground and surface water interaction in natural and disturbed river basins of the cryolithozone of the North-East of Russia, including for solving applied problems, based on permafrost, hydrology, hydrogeology, landscape science and geophysics with applications of remote sensing and field research integrated through mathematical modeling methods. To achieve the goal, the identification of natural and disturbed landscapes using remote sensing data, and key areas for detailed research will be selected. Geophysical and drilling works will be carried out within the sites to establish permafrost-hydrogeological conditions, monitoring stations will be equipped to determine hydrogeological, hydrometeorological and geocryological characteristics, including sampling for isotopic and hydrogeochemical studies. As the main key sites, it is proposed to use the area of the Kolyma water-balance station and the site on Anmangynda aufeis, for which there are long-term observation series in the 20^th century. Field data will become the basis for improving the mathematical model of runoff formation, considering the relationship between groundwater and river runoff in the conditions of permafrost. Mathematical modeling will make it possible to quantitatively analyze the water balance of rivers considering various factors and project water availability both for specific industrial facilities and for the region as a whole.