According to UN experts, by 2030, about half of the world's population will suffer from a shortage of fresh water, and this may cause future hostilities and conflicts. In this regard, extraction of such a valuable mineral as groundwater must be rationally managed. However, practice has shown that managing and protecting groundwater resources is a very challenging task. 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 agreements of the Russian Federation have been identified; a methodology for managing groundwater extraction in the territory of a transboundary aquifer has been developed, dimensions, parameters and factors affecting the formation of a transboundary zone have been determined (using the example of research and analysis of water intake activities in the border territories of the Russian Federation and the Republic of Estonia).