Industrial engineering is one of the major drivers of pressure on water resources and aquatic ecosystems worldwide, where up to 30% of rivers are affected by industrial waste and millions of people experience related health impacts each year. In Kazakhstan, this challenge is aggravated by limited water resources and high concentrations of industrial facilities, while quantitative geoecological assessments of their impact on water catchment areas remain insufficient. This study aims to provide a scientific justification of the impact of industrial engineering on aquatic ecosystems in Kazakhstan and to develop geoecological approaches for improving the stability and management of water catchment areas. Field monitoring, chemical analysis of water and soil, GIS and remote sensing, as well as mathematical modelling were applied to identify the main types and levels of pollution and to assess spatial patterns of impact. The results show that pollutant concentrations decrease from 120 mg/L at the discharge point to 30 mg/L at a distance of 5 km, whereas in several regions the concentrations of heavy metals in surface waters exceed permissible limits by 3–5 times. Modelling indicates that the implementation of green technologies and optimized industrial processes canreduce water pollutants by up to 85% and energy consumption by around 20%, while improving ecological stability indices of water catchment areas. The findings provide a quantitative basis for geoecological management of industrial regions and support the development of integrated monitoring, treatment and regulatory measures for the long-term protection and sustainable use of water resources in Kazakhstan.