Based on a systematic analysis of the structure and dynamics of water resource usage in the catchment area of the Tobyl River basin, the dynamics of the formation of geoecological conditions of water use in the economic sectors within the Kostanay region of the Republic of Kazakhstan were studied. The analysis revealed a significant load from return waters and pollutants, indicating a high and potentially catastrophic pressure that requires regulation of both natural and anthropogenic activities to ensure the region’s sustainable development in the future. A generalized water use scheme for the Kazakh part of the Tobyl River basin was developed, which facilitates the formation of mathematical, physical, and chemical indicators for water management and hydrochemical balance equations. This, in turn, allowed for the creation of a mathematical model of water quality and the determination of the maximum permissible discharge volume of return waters in the river basins. The model ensures compliance with sanitary-epidemiological standards and helps preserve the ecological state of water bodies while supporting the planning of water protection measures to achieve the desired level of water quality in the river.