GIS “Hydromanager” is designed to monitor and manage water quality in the river basin and was created as a project in the desktop general-purpose GIS ArcView GIS 3.2. In this project, taking into account the current regulatory framework, a mathematical model of ecological and economic processes in the natural and technical complex of the river basin is implemented. Implementation of the research on this project continues many years of original research in the field of natural water protection and rational use of water resources. They are based on fundamental developments in the study of hydrological processes dynamics as well as on the development of special computational algorithms and software complexes for creation of appropriate information-modeling tools. A fundamentally new development is the modeling of surface water quality, taking into account their interrelation with groundwater sources. The system under development will include a specialized GIS for surface and groundwater monitoring, containing objective, reliable information and enabling a description of groundwater and surface water status and trends in its change in terms of quantity and quality. In addition, the project envisages the construction of science-based mathematical models of surface and groundwater interrelation based on water and economic monitoring data in the administrative region. The work was awarded the Tyson Prize of the International Association of Hydrological Sciences, which unites more than two and a half thousand specialists from 60 countries.