Groundwater, as a source of water supply, the most important mineral and geopolitical resource, , is often the only source of high-quality drinking water that is protected from pollution under conditions of increasing deterioration of surface water quality. Transboundary groundwaters are the focus of hydrogeological researchers for a number of reasons, including the reduction and pollution of water resources as a result of economic activities. The increased controversy between states over transboundary water issues has necessitated the development of international legal documents on issues related to water conflict prevention and the sustainable use of fresh water. As part of the analysis of the problem of legal regulation of groundwater extraction from transboundary aquifers and complexes, it is proposed to consider this aspect on the example of Russia. The problems of regulation of rational use and protection of fresh water in the bilateral treaties of the Russian Federation were revealed; a methodology for the management of groundwater extraction in the territory of the transboundary aquifer was developed, the size, parameters, and factors influencing the formation of the transboundary zone have been determined (based on research and analysis of water intake activities in the border areas of the Russian Federation and the Republic of Estonia) were determined.