Introduction: Anthropogenic activities artificially increase the concentration of toxic substances in surface reservoirs by discharging polluted water back into the natural environment. Maximum risks for aquatic ecosystems are observed in regions with limited wastewater treatment, which includes Kyrgyzstan. The purpose of the work – research and analysis of factors of pollution of natural reservoirs of Kyrgyzstan by wastewater, consequences for regional aquatic ecosystems and public health, and search for optimal solutions to minimise destructive pollution. Material and Methods: The research was conducted using general scientific methods of cognition, in particular, system analysis, synthesis, generalisation, and concretisation. Results and Discussion: In the course of the research the ecological state of natural water resources of Kyrgyzstan, into which wastewater is discharged, the dynamics of pollution of the aquatic environment depending on various factors of influence is analysed, optimal and feasible to implement measures to reduce the adverse effects of wastewater on the state of natural reservoirs and public health, and improve the overall environmental situation in the region are developed. In addition, the possibilities of applying modern management and technological measures to minimise the content of pollutants in wastewater, based on the synergy of environmental safety and economic efficiency, with the introduction of modern innovative systems of control and monitoring of environmental pollution have been explored. Conclusion: It is established that there is no safe wastewater, therefore, optimisation of the water use and water treatment system in Kyrgyzstan involves the application of an ecosystem approach and the introduction of integrated water resources management.