The article identifies the main directions of the rational use of water resources in the Republic of Kazakhstan, specifically, the South Kazakhstan region. Rational water use is the process of efficient use of water resources, which guarantees the preservation and protection of water bodies from negative and excessive anthropogenic impact and at the same time provides the population and sectors of the national economy with water resources of adequate quality and in the amount that can guarantee not only satisfaction of needs, but also development of industry, energy, water transport and agriculture at the rates that are necessary for sustainable socio-economic development of the Republic of Kazakhstan as a whole. The analysis of the foundations of rational water use was carried out; the main economic instruments affecting the process of water use in Kazakhstan are considered, an overview of the structure of water resources management in the South Kazakhstan region is made. Currently, it is necessary to ensure the rational use of natural resources, their protection from pollution and degradation, as well as skillfully restore, multiply and control them for the benefit of human society. Water resources as an object of management are a complex phenomenon and require a special approach for the formation of governing bodies with a clear division of their sphere of influence and responsibility.